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CasaXPS Manual 2.3.15 Rev 1.
0 Copyright © 2009 Casa Software Ltd
CasaXPS Manual 2.3.15

CasaXPS Processing Software for XPS Spectra
Casa Software Ltd.
NO WARRANTY
Casa Software Ltd. does its best to ensure the accuracy and reliability of the Software and
Related Documentation. Nevertheless, the Software and Related Documentation may
contain errors that may affect its performance to a greater or lesser degree. Therefore no
representation is made nor warranty given that the Software and Related Documentation
will be suitable for any particular purpose, or that data or results produced by the
Software and Related Documentation will be suitable for use under any specific
conditions, or that the Software and Related Documentation will not contain errors. Casa
Software Ltd. shall not in any way be liable for any loss consequential, either directly or
indirectly, upon the existence of errors in the Software and Related Documentation. The
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without warranty of any kind. Casa Software Ltd. further disclaims all implied warranties
including without limitation any implied warranties of merchantability or fitness for a
particular purpose. CasaXPS should not be relied on for solving a problem whose incorrect
solution could result in injury to a person or loss of property. The entire risk arising out of
the use or performance of the Software and Related Documentation remains with the
Recipient. In no event shall Casa Software Ltd. be liable for any damages whatsoever,
including without limitation, damages for loss of business profit, business interruption,
loss of business information or other pecuniary loss, arising out of the use or inability to
use the Software or written material, even if Casa Software Ltd. has been advised of the
possibility of such damages.
Acknowledgements
Casa Software Ltd would like to thank all those providing data and offering
enlightening discussions leading to the current state of the CasaXPS software
and manual. It is a humbling experience to work with so many knowledgeable
people and the author would like to express gratitude to all concerned.
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CasaXPS Manual 2.3.15 Rev 1.0 Copyright © 2009 Casa Software Ltd
Contents
CasaXPS Processing Software for XPS Spectra ..................................................................1
Basics of CasaXPS .................................................................................................................7
CasaXPS Main Window .....................................................................................................7
Loading Data into CasaXPS ...............................................................................................9
Displaying Data in CasaXPS.............................................................................................10
Selection of Data using the Mouse .............................................................................11
Tile Format .................................................................................................................. 12
Tile Display .................................................................................................................. 13
Zooming into Data ......................................................................................................14
Processing Spectra..........................................................................................................17
Basic Energy Calibration .............................................................................................18
Quantification of Spectra ...............................................................................................20
Creating Backgrounds and Regions ............................................................................20
Quantification of Survey Spectrum using Regions .....................................................25
Creating Peak Models .................................................................................................33
Quantification using Standard Reports ......................................................................40
Transferring Regions and Components to other Data ...................................................43
Copying Data to a New Experiment Frame ................................................................49
Annotating Spectra .........................................................................................................50
Quantification of AES Data .................................................................................................56
Differentiation of Spectra ...............................................................................................58
Savitzky-Golay Method ...............................................................................................58
Creating Derivative Spectra for Peak-to-Peak Quantification........................................61
Converting Direct Spectra to Differentiated Spectra .................................................63
Quantification Regions for AES data ..............................................................................66
Creating Quantification Regions using the Element Library.......................................69
Propagation of Quantification Regions ......................................................................71
Quantification Reports ...................................................................................................72
Standard Reports ........................................................................................................75
Custom Reports ..........................................................................................................81
CasaXPS Element Library ..................................................................................................100
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Element Library Format ............................................................................................... 100

Importing a JEOL Element Library ................................................................................ 105
Concentration Calculation ............................................................................................... 106
Auger Imaging in CasaXPS ............................................................................................... 108
Auger Image Analysis Steps in CasaXPS ....................................................................... 111
Ordering the Images using the Experimental Variable ............................................ 112
Copying VAMAS blocks between Experiment Frames ............................................. 114
Converting Images to Differentiated Spectra .......................................................... 116
Quantifying the Spectra at Pixels to Produce Images .............................................. 119
RBD Instruments Inc. Auger Scan .................................................................................... 123
Survey Spectra ............................................................................................................. 123
Multiplex Auger Spectra .............................................................................................. 128
Depth Profile Data........................................................................................................ 129
The Nature of ToF Spectra ............................................................................................... 136
ToF Mass Calibration ....................................................................................................... 138
Calibration Based on Nominal Masses......................................................................... 140
An Example of Mass Calibration using Nominal Masses.......................................... 142
Recalibration of Mass Scale for ToF Spectra ................................................................... 146
Recalibration Steps ...................................................................................................... 148
Peak Fitting ToF SIMS Data .............................................................................................. 149
Line-shapes Suitable for ToF SIMS Spectra .................................................................. 150
Peak Identification and Reduction .................................................................................. 152
IonToF Peak Identification ............................................................................................... 154
Converting IonToF Spectra .................................................................................. 155

Directory Profiling ........................................................................................................ 157
Profile Directory Toolbar Option ..................................................................... 159

Working with ToF Spectra in CasaXPS ............................................................................. 160
Time to Mass Calibration Procedures .......................................................................... 160
Mass Calibration using Regions and Propagation of Regions between Spectra ...... 161
Mass Calibration ....................................................................................................... 162
Propagation of Calibration Regions.......................................................................... 162
Mass Calibration using the Exact Mass Calculator Property Page: .......................... 164
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The Element Library from a ToF Perspective ...............................................................166

The Element Library and Linking ToF Peaks for Display ...........................................167
Profiling Features for ToF data.........................................................................................178
ToF Data File Options ...................................................................................................180
Create a Total Ion Spectrum .............................................................................181

Create Images from Spectra using Quantification Regions ......................................183
Spectra Generated from Image Zones......................................................................185
Creating a Profile from a Total Ion Spectrum ...........................................................187
Spectra Generated from Profile Layers .............................................................189
Create a Profile from a Directory of Files ..........................................................189
Convert and Merge a Directory of XYT File .......................................................192
Image Depth Profile Data Analysis ...............................................................194

Quantification Reports and ToF Data ..............................................................................197
Quantification via the Report Spec Property Page ......................................................197
Standard Report ........................................................................................................198
Custom Report ..........................................................................................................201
An Overview of Working with ToF Data in CasaXPS ........................................................203
SIMS Toolbar Buttons: Display Options........................................................................203
An Overview .................................................................................................................210
Basics of CasaXPS..........................................................................................................212
Converting Data ........................................................................................................212
Data Viewed Via an Experiment Frame ....................................................................213
Displaying Data .........................................................................................................214
Selecting VAMAS Blocks ...........................................................................................215
Tile Display Options ..................................................................................................216
Display Colours .........................................................................................................217
Calculating SNMS Sensitivity Factors ...........................................................................219
Quantification of SNMS Profiles ...................................................................................229
Quantification of Stainless Steel using SNMS: an Example ......................................229
Specifying the Sputter-Rate ......................................................................................234
Creating a Calibrated SNMS Profile ..........................................................................235
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Dynamic SIMS .................................................................................................................. 240

Notes on Dynamic SIMS RSF Calculation ..................................................................... 241
Reference Signal Measured during the Course of Profile ........................................ 241
Reference Signal Measured at End of Acquisition Cycles ........................................ 242
Quantification of Dynamic SIMS Profiles ..................................................................... 243
Quantification of Basic Profiles ................................................................................ 245
Making Adjustments to the Sputter Rate ................................................................ 256
Display of Calibrated Profiles ................................................................................... 257
Further Aspects of Dynamic SIMS Quantification........................................................ 258
Logical Structure of a SIMS Depth Profile within CasaXPS ....................................... 258
Methods for Computation of RSF and Sputter Rate Values .................................... 259
Identification of the Matrix and Interface Cycles .................................................... 259
Selecting Ranges of Cycles on the Calibration Property Page.................................. 263
Surface Data and Background Signal........................................................................ 264
Three Ways to Calculate RSF Values from Standard Samples ................................. 265
Adding RSF and Sputter Rates to Profile Data ......................................................... 266
Applying Calibration Parameters to One or More Profiles ...................................... 266
Depth Profile Statistics: Areal Density and Decay Length ........................................ 267
Maintaining Standards Library Files ......................................................................... 268
Step-by-Step Description of Quantification for a Multi-Layer Sample .................... 268
An Example of Computing an RSF using Dose and Implant Peak Depth.................. 274
Computing RSFs where the Matrix Signal is Measured following the Completion of the
Implant Profile .......................................................................................................... 276
Gathering Profile Data for Display and Calibration Purposes...................................... 278
Electron Spectroscopy ..................................................................................................... 282
Quantification of Spectra using Transmission Correction ........................................... 283
Practical Solutions to Transmission Correction ........................................................... 287
Adding a Transmission Function to SPECS SpecsLab1 Data......................................... 288
Adding a Transmission Function to Data Blocks .......................................................... 290
Add Transmission Function from File ....................................................................... 291
Relative Sensitivity Factors and Instrument Geometry ................................................... 292
PHI Multipak Data ............................................................................................................ 294
Quantification of PHI Spectra ...................................................................................... 297
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Creating a PHI Library ...............................................................................................298

Creating Quantification Regions ...............................................................................303
Quantification of Thermo Scientific Data.........................................................................312
Converting Avantage Data............................................................................................313
Thermo Scientific Avantage Files ..............................................................................314
Merging Sets of Experiments .......................................................................................315
Quantification ...............................................................................................................316
Element Library Excitation Source String .....................................................................317
Transmission Function ..................................................................................................318
Preparing an Element Library for use with the K-Alpha...............................................319
Quantification of JEOL XPS Spectra from SpecSurf ..........................................................322
XPS Spectra.......................................................................................................................325
Other Peaks in XPS Spectra .......................................................................................330
Basic Quantification of XPS Spectra .................................................................................331
How to Compare Samples ........................................................................................333
Relative Intensity of Peaks in XPS .............................................................................333
Overlapping Peaks ....................................................................................................335
Peak Positions ...........................................................................................................337
Charge Compensation ..............................................................................................337
Depth Profiling using XPS .................................................................................................339
6
Basics of CasaXPS
The following is an introduction to the basics of CasaXPS. The intention is to
provide an overview of the software in terms of displaying and quantifying
XPS spectra.
CasaXPS Main Window
The Main Window of CasaXPS is a multiple document interface capable of

managing large numbers of files all open at the same time.
Key points:
Each file opened in CasaXPS appears in an experiment frame.
The top-most experiment frame has mouse focus.
An experiment frame is divided into two panes; the left-hand pane
displays the data in graphical form, while the right-hand pane displays
the logical structure of the VAMAS file opened in CasaXPS.
Management of experiment frames is performed using the Window menu on
the CasaXPS main window.
7
Experiment frames may appear full sized.
Experiment frames may be tiled.
Or as icons within the CasaXPS Main Window.
8
Loading Data into CasaXPS

CasaXPS converts other data formats to ASCII ISO 14976 (VAMAS) format.
Data in VAMAS format are opened as experiment frames by selecting the
VAMAS file via the Open option on the File menu.
A file dialog window allows data to be selected from disk.
Data not in VAMAS format is converted through CasaXPS via the Convert
option on the File menu. A Convert to VAMAS file dialog window offers a
means of selecting a file type for conversion. The file extension is typically
used to determine the file format, for example, the file extension spe is
allocated to data saved in PHI Multipak format.
9
A new VAMAS file is created for each file selected via the dialog window and
is written into the same directory as the original file.
Displaying Data in CasaXPS

One or more files may be selected via the file dialog. On pressing the Open
button, a new experiment frame appears in the CasaXPS main window.
Initially, the first row of data blocks are selected in the right-hand pane
and displayed via a scrolled list of display tiles in the left-hand pane.
10
The keyboard arrow keys can be used to change the selection in the right-
hand pane. Each press of an arrow key moves the selection in the right-hand
pane with respect to the data block displayed in the active tile in the left-
hand pane. Pressing an arrow key causes the newly selected data block to be
displayed in the left-hand pane.
Selection of Data using the Mouse
Data blocks in the right-hand pane are selected using the mouse and a
combination of the Shift key and the Control key.
Left click the mouse over a data block in the right-hand pane to make a single
selection.
Extend the selection to a contiguous group of data blocks by holding the Shift
key down before selecting a second data block using the left mouse button.
11
Add to the current selection by holding the Control key down before left-
clicking over a data block.
Overlay the current selection of data blocks in the active tile by pressing the
overlay toolbar button.
Display the current selection one-per-tile using the display toolbar button.
Tile Format
Set the number of tiles-per page using the Page Tile Format dialog window.
12
Page tile formats are organized using predefined property pages for a
number of tiles per page. Adjustments to the tile format involve choosing the
tile alignment type.
Specifying the number of rows (or columns):
Specifying the number of tiles per row for each row enabled:
Tile Display
Each tile used to display data in the left-hand pane maintains a set of display
settings. These display settings are adjusted using the Tile Display Parameter
dialog window. Various fonts and colours used to draw spectra are adjusted
via the property pages on the dialog window.
13
The tile in the left-hand pane with the title highlighted is the active tile. On
pressing the toolbar button for the Tile Display Parameters dialog window,
the settings entered onto the property pages correspond to the display
settings for the active tile. When the OK or Apply button is pressed on the
dialog window, the display settings for the active tile are updated.
Data displayed in the active tile is indicated in the right-hand pane by a red
border around the corresponding data block. The background for the data
block in the active tile is also filled with a light yellow colour.
Zooming into Data

Changing the energy and intensity ranges for a spectrum is achieved using
the mouse to draw a zoom box over the data currently displayed in the active
tile. A zoom box is drawn over the data by holding down the left-hand mouse
button whilst moving the cursor over the spectrum in the active tile. On
releasing the mouse button, the drag box becomes a solid box over the data
marking the energy limits and also the intensity limits over which it is desired
to view the data.
14
To perform the zoom action, left-click inside the zoom box or press the zoom
in toolbar button on the second toolbar.
Each time a zoom action is performed, the parameters from the zoom box is
placed on a zoom list. Following a sequence of zoom actions, the set of zoom
states on the zoom list can be reviewed by pressing the zoom out toolbar
button.
Each time the zoom out button is pressed, the previous energy and intensity
ranges defined by zoom boxes are reinstated sequentially until the initial
display ranges first used to view the data are recovered. Further pressing of
the zoom out button will cause the zoom list to cycle from the initial zoom
state.
The zoom list is re-initialised by pressing the reset toolbar button:
If the data are prepared with quantification regions, pressing the reset
button loads the zoom list with the quantification region limits. To view a set
of peaks on a survey spectrum for which regions are defined, simply press the
reset button followed by the zoom out button.
Reset Zoom out
15
Loads regions Step to region
Return to the initial display state.
Zooming into a zone based on the mouse may require further adjustments to
the display to achieve the desired perspective of the data. Further intensity
scaling and positioning of the data with respect to the energy axis are
achieved using the toolbar buttons:
Adjustments to the energy interval accompanied by rescaling of the intensity

with respect to the data within the energy interval are performed using the
toolbar buttons on the second toolbar:
16
Drag zoom box over Zoom in

data of interest.
Or
Left-click inside zoom
box.
Step right
Energy interval shifted

by half the display width.
Rescaling using the data within the current energy interval is achieved using
the toolbar buttons:
Processing Spectra
Processing spectra is performed using options on the Spectrum Processing
dialog window. The Spectrum processing dialog window is invoked from the
Options menu or the top toolbar.
17
The Processing History property page lists the processing currently

contributing to the state of the data displayed in the active tile. Other
property pages offer processing options such as charge compensation and
data smoothing.
Basic Energy Calibration

Shifting the energy scale to allow for sample charging is performed on the
Calibration property page:
There are many powerful methods for charge compensating data located in
many different files or sets of data within the same file, for example a depth
profile. Only the basic charge compensation is described here.
Essentially, charge compensation is performed by specifying the location of a

peak in the data as recorded. The measured location of the peak is associated
with the desired true location of the peak, from which the necessary shift is
18
determined. The calculated shift may be applied to one or more spectra as

appropriate.
Charge Compensation for a Set of High Resolution Spectra

Display the spectrum for which a peak position is known:
Using the mouse, left-click the cursor on the peak as displayed in the active
tile. The energy identified by the cursor position is updated in the Measured
text-field on the Calibration property page.
Enter the known value for the peak position in the True text-field.
If regions and/or components are defined on any of the VAMAS blocks for
which charge compensation will be performed, tick the Region and
Component tick boxes.
Select those VAMAS blocks for which the charge compensation shift is
appropriately specified by the data in the active tile.
19
Press the Apply to Selection button.
Each VAMAS block selected in the right-hand pane of the experiment frame
will be shifted using the energy difference computed from the Measured and
True text-fields on the Calibration property page.
Quantification of Spectra
XPS quantification in terms of peak intensities is performed by assigning
quantification regions and/or peak models containing synthetic components.
Quantification in CasaXPS is performed using the Quantification Parameters
dialog window where the Regions, Components and Report Spec property
pages are central to preparing and extracting quantification information from
the data.
Creating Backgrounds and Regions

Quantification regions are energy intervals over which a background to the
peaks is defined.
20
A region is defined using the Regions property page where each region
appears as a column of parameters in a scrolled list.
Each column in the scrolled list is divided into editable parameters and
quantities computed for the region defined by the parameters.
21
To edit a region parameter, left-click the mouse over the value displayed on
the table on the Regions property page.
The value modified within the edit text field is only accepted when the enter
key is pressed on the keyboard. Before pressing the enter-key, left-clicking
the mouse away from the edit field causes the previous value to be
reinstated.
Regions are defined in terms of a regions name:
Region names are user-defined names used to reference the information

determined from the region. Quantification tables typically include the region
name and more importantly quantities calculated from a region are specified
within custom reports using the names assigned to a region.
A Relative Sensitivity Factor or RSF for a peak identified by a region is

typically extracted from the element library, but may be adjusted using the
RSF row.
Atomic concentration tables are computed from the raw peak area divided
by the RSF parameter. Other corrections to the raw peak area are also
applied when determining the atomic concentration; however the
instrumental independent correction used to relate the relative intensity of
different photoelectric transitions for an element is encapsulated in the RSF.
The start and end parameters define the energy interval over which a peak
should be measured.
22
These energy limits define the point at which the background meets the
recorded data.
A range of background (BG) types are offered, the most commonly used
types are linear, Shirley and Tougaard.
Linear backgrounds are typically used for insulating materials, while steps in
metallic data are modelled using a Shirley background.
23
The full set of background types can be selected via a dialog window invoked
by holding the Control key down and left-clicking over the current BG-type
setting before the parameter is an edit field.
A new background is selected from the list on the dialog window and is
loaded into the BG type text field when the OK button is pressed. To accept
the selection of the background type, press the enter key on the keyboard.
The BG type field may be typed into the edit-field as an abbreviation. The
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The background and spectrum meet at the two energy limits to the region.
Due to noise in the data, the actual data channel corresponding to the region
limits may not be most appropriate for defining the background intensity at
these limits. The Av Width parameter specifies the number of data channels
on either side of the data channel corresponding to the start energy or the
end energy over which an average intensity is determined for the background
at the limits.
24
When using the Av Width parameter there must be sufficient data channels
to either side of both start and end limits before the background intensity is
determined using an averaged intensity. The largest source for precision
errors in XPS measurements is due to poorly defined background intensities.
The use of an appropriate Av width for the level of noise in the data is
important.
Two additional parameters influence the intensity of the background at the

region limits. The start offset and end offset provide a means of scaling the
background intensity at the region limits. The value specified for these
parameters represents a percentage drop from the initial intensity computed
for the background intensity.
The cross section and tag fields are for advanced uses and therefore are not
discussed here.
Quantification of Survey Spectrum using Regions

The best route to creating quantification regions is via the Element Library
dialog window. The advantage of using the element library lies in the direct
link between specifying the peaks and the RSF scaling information from the
library. The simplest route to creating quantification regions is via the Find
Peak/Create Regions buttons on the element table property page.
25
Regions are created via the Create Regions button for all those features on a
spectrum for which:
1. An element marker from the element library is active.
2. A feature within the data can be identified.
3. The RSF is the largest or the transition is explicitly selected for use via
the CasaXPS_quant.lib configuration file.
Using the element library dialog window , the first step is therefore to
enable element markers for all the appropriate species within the data. The
manual route to enabling element markers involves the element table, the
left-hand pane and the mouse. With the Element Table property page top-
most on the Element Library dialog window, left-click the mouse with the
cursor pointing at a peak in the data. The element table scrolls to display
those transitions with energies around the energy indicated by the mouse.
Select the most likely transition from the table on the Element Table using
the name field.
26
Element markers are placed on the data for all transitions in the element
table from the indicated element. The process is repeated for each peak in
the data until all peaks are assigned to element markers.
27
Regions are created based on the proximity of element markers to the peaks
in the data. In the event the energy scale needs calibrating, the calibration
step should be performed before attempting to create regions.
To calibrate the energy scale for an individual spectrum:
Select the Spectrum processing dialog window
Select the Calibration property page
Left click the cursor pointing at the peak maximum of an appropriate peak in
the left-hand pane and enter the True energy for the indicated peak.
Press the Apply button to calibrate the spectrum in the active tile.
28
Provided the peaks are within a tolerance of the element markers and the
peaks of interest are accounted for by the element markers, pressing the
Create Regions button on the Element Table property page will create a set
of regions on the spectrum.
An annotation table offering a quantification table is added to the spectrum.
The element markers used to identify and link the peaks to transitions in the
element library may be removed from the display by pressing the Clear All
Elements button on the Element Table property page.
The quantification table may be repositioned on the data using the

Annotation History property page.
29
With the Annotation History property page top-most on the Annotation

dialog window, a small box appears above the top left-hand corner of the
annotation table.
Pointing at the centre of the small box then dragging the mouse causes the
annotation to move to a new position the moment the mouse button is
released. Other adjustments to the intensity scale for display purposes can be
made using toolbar buttons.
It is also advisable to check the quantification regions created automatically

on the data. The zoom options described above provide a means of
systematically stepping through the current list of quantification regions. If
the Regions property page on the Quantification Parameters dialog window is
top-most, stepping through the set of regions using the zoom options allows
30
the limits for the regions to be visually inspected and adjusted under mouse
control.
Adjusting the limits for a region under mouse control involves using the
mouse to drag a limit to a new position. Region limits can be adjusted under
mouse control only when the Region property page is top-most on the
Quantification Parameters dialog window. A grey vertical zone indicates that
the mouse is active with respect to adjusting the region end points.
Following an adjustment to the limits, the annotation table and Regions

property page are updated with the start and/or end energies defined by the
cursor.
31
Manual Creation of Regions

Regions created based on element markers require an identifiable peak to
exist. If no such feature is located near the element markers no region is
created for the element in question. Under these circumstances manual
creation of regions is appropriate. While a Create button is available on the
Regions property page of the Quantification Parameters dialog window,
peaks from a survey spectrum have no means of assignment to transitions;
therefore the Element Table property page includes a feature for manually
creating regions specified via the name field in the element table.
To create regions one at a time:
1. Invoke the Quantification Parameters dialog window and ensure the

Regions property page is top most
2. Tick the box on the Element Library dialog window on the Element
Table property page labelled Create When Line Selected.
3. In the active tile, zoom the display to the energy interval about the
transition for which a region is required.
4. Left click the name field on the Element Table appropriate for the
transition.
32
Adjust the start and end limits using the mouse or otherwise position the
region appropriately for the transition selected.
Creating Peak Models

Constructing a peak model requires the definition of a background using the
Regions property page and the introduction of synthetic component peaks
via the Components property page.
The Regions property page is used to define a background to the data

envelope.
The intensity from a quantification region can be explicitly excluded from a

quantification report by entering an RSF of zero.
33
The function of the region is to define the background only allowing the
intensities from the synthetic components to estimate the sample
composition.
Components are created using the Element Table property page in an

analogous way to the method for creating individual regions. Left-click the
mouse with the cursor over a peak as displayed in the left-hand pane. The
Element Table scrolled list changes to display those transitions around the
energy indicated by the cursor.
Tick the box on the Element Table property page labelled Create When Line
Selected. With the Components property page top-most on the
Quantification Parameters dialog window, left-click the appropriate name
field within the element table for the transition identified in the left-hand
pane.
34
A peak is added to the display and the Component property page is updated.
New peaks are added to the data where the residual is the greatest. The new
peak is therefore unlikely to appear in the correct position with respect to
the peak envelope. Using the mouse, point at the peak maximum for the
newly created peak and drag the cursor to the appropriate position for the
synthetic component.
Repeat the process for each peak believed to be part of the model.
35
The example involves two elements and potentially five chemical states: one
chemical state for the potassium and four for the carbon data. The two
potassium peaks are part of a double pair; therefore the RSF for the
combined pair of peaks is used when quantification is performed.
While it would be possible at this stage in the peak modelling process to

press the Fit Component button on the Component property page, the
number of peaks and level of noise in the data suggests that constraints will
36
be required to achieve a valid physical description based on non-linear least

squares peak fitting.
A peak model is defined in terms of a name field and RSF serving exactly the
same function as the name and RSF fields for regions. Fields specific to
components are the line-shape parameter and the three parameters for area,
position and full width at half maximum (FWHM) of the synthetic
component. The parameters determined in a least squares sense are the
area, position and FWHM. Constraints are available for restricting the
possible values for these parameters during optimisation.
Constraints take two forms:

1. Parameter intervals offering a range of acceptable values for each
parameter adjusted during a least squares optimisation.
2. Relational constraints between parameters from different
components.
An interval is specified as a pair of numerical values separated by a comma:
Relational constraints involve specifying a parameter as related to a

parameter from a second component in terms of an offset or a factor. For
37
example, the area ratio of two peaks from a p-orbital doublet pair is in theory
2:1. To impose this theoretical relationship for a potassium doublet, for
example, the following constraint forces the 2p3/2 peak to be twice the size of
the 2p1/2 peak:
Relational constraints are defined in terms of the column header letters, thus
to force the area of the peak in column A to be half the area of the peak in
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can be defined as a factor constraint, while a position constraint is defined in
terms of an offset to a second parameter.
Line Shapes
CasaXPS offers many different functional forms for synthetic components.
The line-shapes are specified using strings entered into the line-shape field
on the Components property page. Line-shapes are described in detail
elsewhere in the CasaXPS manual; however the most commonly used
synthetic line shapes are product Gaussian-Lorentzian GL(m) and sum
Gaussian-Lorentzian SGL(m), where m=0 is a pure Gaussian and m=100 is a
pure Lorentzian shape.
38
The line-shape LA(a,b,n) offers asymmetric line-shapes based on the

Lorentzian functional form convoluted with a Gaussian.
A useful means of monitoring complex peak models is via a components

annotation table displayed over the data.
Exporting Peak Models as Data
39
Peak model data are exported via the clipboard. Display the VAMAS block for
which a peak model is prepared in the active tile and press the toolbar
button. A clip board selection dialog offering a table of data, where the table
includes columns for binding energy, kinetic energy, spectral data in CPS,
component data, the background intensities and the total synthetic
envelope. These data can be saved as a TAB spaced ASCII file or copied onto
the clipboard and pasted into software capable of accepting text data
through the clipboard.
Quantification using Standard Reports

Quantification reports are text-based information generated from
quantification regions and/or components defined on VAMAS blocks. The
most common form for a quantification report is a tabulation of atomic
concentrations calculated from regions on survey spectra.
40
The Report Spec property page on the Quantification Parameters dialog

window provides the means of creating quantification reports from VAMAS
blocks selected in the right-hand pane of the experiment frame. Creating a
quantification table from regions on a survey spectrum involves:
1. Defining a configuration file.
2. Selecting the VAMAS block in the right-hand pane of the experiment
frame.
3. Pressing the Region button in the Standard Report section of the
Report Spec property page.
The configuration files for the Standard Report section are a set of ASCII files
located in the CasaXPS.DEF directory. These configuration files contain
keywords, one per line, specifying the type of information included in the
columns of the text base report. The configuration file for the Standard
Report Regions button is called RegionQuantTable.txt.
The keywords listed in the file RegionQuantTable.txt are used to arrange the
columns of the quantification report provided the Use Config File tick-box is
ticked.
41
Selecting the VAMAS block in the right-hand pane before pressing the Region
button causes a new view into the experiment frame to appear within the
CasaXPS window.
The quantification table displayed in the new window can be copied through
the clipboard or saved to disk by pressing the Copy toolbar button. Once on
the clipboard, any program capable of accepting text from the clipboard may
receive the data by requesting a paste action (usually Control-V).
42
To return to the experiment frame displaying the spectra either switch

windows via the Window menu of CasaXPS or close the text report window.
Similar configuration files are available for configuring reports for each of the
buttons in the Standard Report Section.
Transferring Regions and Components to other Data

Depth profiles are just one example of data sets where quantification
information needs to be propagated throughout a set of similar spectra. The
techniques described below are equally applicable to data from a range of
experiments and apply to data spread over many VAMAS files as it does for
data collected into a single experiment frame.
The propagation of quantification information to other spectra will be

discussed using an example of a depth profile performed on a multi-layer
material.
The data set consists of a set of survey spectra measured following a

sequence of etch cycles. To examine the change in composition with etch
time, the survey spectra require quantification regions appropriate for the
entire set of spectra. Ultimately, each spectrum in the profile will have
43
regions defined on it and therefore minor adjustments on a spectrum-by-

spectrum basis are possible; however to obtain a reasonably good initial set
of regions, the spectra are overlaid in the active tile so that all variations of
the peaks can be assessed whilst defining the regions.
Create a region for each line in the survey spectrum representative of the
elements present. First create a region for the O 1s peak using the element
table method described above. Two chemical states of oxygen are clearly
present in the data; however a single region will monitor the amount of
oxygen in the profiled material.
Zoom into the Ti 2p peak envelope and add a region to measure titanium
based on the Ti 2p peaks.
Similarly add regions for carbon and silicon.
44
The regions as the data stands are all defined on the first spectrum displayed
in the active tile. The next task is therefore to propagate the regions from the
first spectrum to the remaining set of spectra.
Ensure the spectrum for which the regions are defined is displayed in the
active tile in the left-hand pane.
Select the set of survey spectra in the right-hand pane.
Move the cursor over the active tile displaying the spectrum for which the
regions are defined and right-click the mouse. A Browser Operations dialog
window lists the set of selected VAMAS blocks. Tick the Regions tick-box in
the Propagate sections and press the OK button.
45
A progress dialog may appear briefly and on completion, the regions are
transferred to the selected VAMAS blocks.
The objective for a depth profile is to display the variation of the signal as a
function of depth. For this example, the depth will be measured in terms of
etch-time; nevertheless, the type of report required to produce the profile
differs from the format obtained from the Standard Report. To generate a
profile as a function of time, the Custom Report section on the Report Spec
property page is employed.
46
The custom report is designed for profiling experiments. The set of

quantification items (regions and components) defined on the selected
VAMAS blocks are listed in the Quantification Item Names table. From these
quantification item names a set of named formulae are prepared.
NB: The name fields are used to define the relationships between the
intensities in a profile. A special relationship is automatically applied to any
quantification items assigned the same name. Specifically, if two
quantification items have the same name then the intensity for the items
with the same name are added together. It is therefore very important to
name regions and components with different names whenever a custom
report is used.
Since the current example includes only regions, pressing the Region button
transfers the region names into the table of names and formulae.
47
On pressing the Apply button in the Custom Report section, a column

orientated quantification report is generated.
The text based report may be transferred through the clipboard to other
programs or plotted within CasaXPS either as a separate file or appended to
the current VAMAS file. Appending the profile data to the current file allows
cross referencing the profile to the spectra. Both options are available on the
File menu offered when the profile is tabulated.
Choosing the Add Profile menu option on the File menu adds the profile data
to the original spectra as a temporary additional VAMAS file. The presence of
a profile file is indicated in the bottom left-hand corner of the active tile.
48
To switch between viewing the spectra and the profile derived from the
spectra, press Control-F8 on the keyboard. The profile view of the data set
can be used to mark a set of etch times using a cursor drag-action coupled
with holding the Shift Key down; on switching the display to the spectra using
Control-F8, the set of etch times marked by the cursor become selected.
Similarly, a contiguous selection in the spectrum view will determine the
location of a cursor on the profile view of the data.
Copying Data to a New Experiment Frame

The depth profile VAMAS file continues to only contain the spectral data
even after the Add Profile menu option is applied. To preserve a profile the
VAMAS blocks containing the profile traces must be copied to a new
experiment frame. The new experiment frame can be saved once populated
with the profile VAMAS blocks. To copy VAMAS blocks between experiment
frames:
1. Select the VAMAS blocks in the right-hand pane.
2. Either, create a new experiment frame using the File menu or toolbar
button, or switch focus to an existing experiment frame.
3. Press the Copy and Paste VAMAS blocks toolbar button.
4. Press the OK button on the Copy Selected VAMAS blocks dialog
window.
49
The new experiment frame contains a copy of the VAMAS blocks.
Annotating Spectra
Text and tables are added to spectra via the Annotation dialog window.
50
Text may be added to the display as individual items of annotation. Each

piece of annotation appears in a list on the Annotation History dialog
window. The list allows the annotation items to be selected, amended and
deleted using the options on the Annotation History property page.
The position of the annotation on the display is indicated by a small box next
to the annotation text. Pointing the cursor at the box and dragging the cursor
to a new position causes the annotation to move the moment the mouse
button is released.
Modifying a piece of annotation involves selecting the annotation in the

Annotation History list.
To alter the font, press the Font button and choose a new font for the
selected annotation item.
51
Press the OK button on the Font dialog window and then press the Apply
button on the Annotation History property page.
To adjust a specific annotation item, left-click the box located next to the
annotation on the display. As a result, the annotation item is to move to the
top of the list on the Annotation History property page.
Initially Ce LMM text is not visible in the scrolled list without scrolling through
the list.
52
Left click the box beneath the Ce LMM annotation text on the display in the
left-hand pane. Clicking the box causes the annotation item to move to the
top of the list.
Select the Ce LMM item on the Annotation History property page. To make
the annotation horizontal rather than appearing in the initial vertical
orientation, un-tick the Vertical Text tick-box and press the Apply button.
53
Auger Spectroscopy
Auger peaks in an energy spectrum are an indirect consequence of the
excitation of core level electrons. Subsequent relaxation of the excited state
induced by the interactions of a primary electron with an atom may result in
the emission of an electron with a characteristic energy. These Auger
electrons appear superimposed on a background of secondary and
backscattered electrons.
The energy from the excitation source, typically an electron gun, alters the
electronic state of an atom within the surface by ejecting a core level
electron. The relaxation of the excited state occurs as a separate event from
the core level excitation, so the characteristics of the excitation source have
no influence on the energy with which Auger electrons are ejected from the
surface. Auger electrons for an atom in a given chemical state always have
the same energy regardless of the energy imparted by the primary electron
beam or even when excited by other means such as x-rays. An oxygen Auger
line, O KLL for example, appears at the same kinetic energy in a spectrum for
both electron bombardment induced Auger or XPS induced Auger, regardless
of the anode material in the x-ray gun.
Thanks to Tyne R. Johns of Sandia National Laboratories for her assistance in editing this manuscript.
Data used in the preparation of this text are kindly provided by:
Prof Bridget Rodgers (Vanderbilt University)
Tyne R. Johns (Sandia National Laboratories)
Data provided courtesy of Sandia National Laboratories. All rights in the data are reserved by the US Government. Neither the US Government nor Sandia
Corporation makes any warranty, express or implied, or assumes any liability with respect to the use of these data, and publication of these data does not
constitute express or implied endorsement of any kind.
RBD Instruments Inc.
IFOS, Kaiserslautern , Germany
54
Auger peak intensities do depend on the excitation source and therefore

Auger element libraries must include relative sensitivity factors for the
specific electron gun energy used to excite the surface material.
The Auger mechanism involves exciting a core electron followed by the decay
of an outer electron to fill the core level. The new electron configuration is
energetically unstable and results in the emission of energy by ejecting an
electron with an energy characteristic of the intermediate states. These
Auger transitions are often labelled using the letters assigned to the principal
quantum numbers for the electronic shells: K, L, M, N, ... with subscripts
differentiating the sub-shell structure.
55
For a more complete description of the Auger mechanism see Briggs and
Grant ISBN 1 901019 04 7.
Auger Electron Spectroscopy (AES) is performed using a Concentric
Hemispherical Analyser (CHA or HSA) or a Cylindrical Mirror Analyser (CMA).
The AES technique is offered in a stand-alone form and also as a multi-
technique instrument, often including XPS to complement the advantages of
AES. Sub-micron spatial resolution requires a means of isolating vibrations
and Mu-metal shielding from stray electric and magnetic fields.
The following is concerned with spectra acquired using a CHA operating in

fixed retard ratio mode or a CMA.
Quantification of AES Data

The acquisition mode for AES data determines the characteristics of the
spectra and hence the quantification of peak intensities. CHA instruments
typically have a response as a function of kinetic energy which behaves as an
inverse power of the kinetic energy
56
where the exponent n is typically in the range 0.5 to 1. Historically AES

spectra are measured using a fixed retard ratio FRR mode for the CHA. The
FRR mode records the number of electrons reaching the detector as the
kinetic energy of the ejected electrons is stepped such that the ratio of the
initial kinetic energy of the electron to the pass energy of the analyser is
maintained as a constant during the acquisition. A consequence of using FRR
mode is that the energy resolution of the data changes with kinetic energy so
that at high kinetic energy where the response of the CHA is reduced, the
energy width accepted by CHA increases; the signal accepted by the CHA for
electrons emitted with higher kinetic energy is greater than for lower energy
electrons. The resulting spectra are therefore more uniform in intensity over
a wide energy range. In particular, the high yield of secondary electrons at
low kinetic energies is attenuated by the FRR mode, thus protecting the
detector system from excessive count rates. As a result of these practical
considerations, AES data are more difficult to quantify in terms of peak areas,
therefore the method used to quantify Auger spectra is to measure the
intensity of a transition using a differentiated spectrum, determining the
peak intensity by the difference in the positive and negative going derivative
peak heights.
The so called direct spectra, as recorded, must be numerically differentiated

to provide the data in a form suitable for quantification in terms of peak to
peak intensities.
57
Some instruments, in keeping with the past, acquire the data using hardware
signal differentiation, which partially accounts for the quantification based on
peak-to-peak intensities. Most AES spectra acquired from modern
instruments are in direct mode and so must be numerically differentiated
before quantification is performed.
The energy window for a CMA instrument is proportional to the kinetic
energy of the analysed electrons. The CMA acquisition characteristics are
therefore equivalent to data acquired using a CHA in FRR mode.
Differentiation of Spectra
Differentiating data in which noise is a component requires the use of a more
subtle approach than Newton-Cotes differentiation. A least squares approach
attempts to mitigate the influence of noise on the resulting derivative.
Savitzky-Golay Method
Two options on the Spectrum Processing dialog window commonly used for
smoothing of experimental data and the determination of derivatives are
performed using the algorithm proposed by Savitzky and Golay (A. Savitzky
and M. J. E. Golay, Anal. Chem., 36, 1627 (1964)). The same algorithm is
employed to differentiate spectra as is used to smooth data and therefore it
should be clearly understood that the act of differentiating a spectrum using
the Savitzky Golay method necessarily includes a smoothing operation.
58
Theory
Given a set of data containing both signal and noise, the initial objective of
the Savitzky-Golay method is to replace the raw data by a smoother set of
data representing the true signal responsible for the record intensities. For a
constant underlying signal, the most natural means of estimating the true
signal from a set of measurements would be to average the values. The act of
averaging a set of values is in fact one example and possibly the simplest
applications of the linear-least-squares principle. Spectral data, on the other
hand, typically contain peaks superimposed on a background signal and
therefore a more subtle use of averaging is required if the essential structure
in the data set is to be retained. One way to use the averaging process, but to
maintain information relating to the variation in the intensities, is to perform
a local averaging for each bin within a spectrum; for example, each data bin
could be replaced by the average of three bins, the bin itself and the two bins
on either side of the bin. The averaging operation could be applied to a data
set via a digital convolution of the data bins with a convolution kernel
consisting of the values {1/3, 1/3, 1/3}. These simple, yet often used concepts
are at the basis of the Savitzky-Golay method, which in essence applies the
least-squares principle to determine an improved set of kernel coefficients
for use in a digital convolution, where these improved coefficients are
determined, in the least-squares sense, using polynomials rather than, for
the case of averaging, simply assuming a constant value determined from a
sub-range of data bins. Indeed, the Savitzky-Golay method could be seen as a
generalisation of averaging data, since averaging a sub-range of data
corresponds to using a Savitzky-Golay polynomial of degree zero.
To illustrate the Savitzky-Golay method, consider the specific example in
which five data bins are used to approximate a quadratic polynomial. The
polynomial can be expressed in the form:
where the coefficients a0, a1 and a2 are determined from the simultaneous
equations in which the abscissa x is the index for the data bin; the origin is
always placed at the central data bin, thus the abscissa values corresponding
to each of the data bins are {-2, -1, 0, 1, 2}:
59
or
where the evenly spaced data bins {d-2, d-1, d0, d1, d2} are selected with the
target of replacing the value for d0 with the value for the polynomial at x = 0
or p(0) = a0. Since there are five equations and only three unknowns, the
coefficients to the polynomial must be determined in the least-squares
sense, where the linearly independent basis functions are 1, x and x2. The
normal equations yield:
Since ATA is a square symmetric matrix of rank three, the coefficient vector a
is determined from [ATA]-1AT, the top row of which yields the prescription for
computing the value of a0, namely:
Thus, for each set of five such data bins, the central bin can be replaced by
the value determined for a0. In other words, a digital convolution using the
five point kernel {si} and the raw data bins results in a smoothed set of data
bins, where a linear least squares quadratic polynomial is used to model the
data, five channels at a time.
Similarly, the derivative of a spectrum can be computed using the Savitzky-
Golay polynomial. Again the intention is to approximate the derivative at a
given point in the spectrum using the derivative of the polynomial at x = 0.
Since dp(0)/dx = a1, the second row of the matrix [ATA]-1AT yields a second
convolution kernel for computing the derivative of the spectrum and, apart
from the difference in the kernel values, the computation of the derivative
proceeds in an analogous fashion to that of the smoothing calculation.
60
Creating Derivative Spectra for Peak-to-Peak

Quantification
Direct spectra are converted to differentiated spectra using the Spectrum
Processing dialog window.
The Differentiation property page on the Spectrum processing dialog

provides a choice of two Savitzky Golay methods and a smoothing width
value. The parameters used in the Savitzky Golay differentiation option
depend on the source of the relative sensitivity factors used to quantify the
data. For example, the set of RSFs in Appendix C of Briggs and Grant are
designed for data acquired using an energy step size of 1 eV and
differentiated using a 5 point quadratic Savitzky Golay differentiation
method. Matching the acquisition step size and Savitzky Golay parameters is
important because these influence the peak-to-peak height determined for
an Auger peak. Consider a Gaussian peak with a FWHM of 7 eV tabulated at 1
eV and 0.5 eV step-sizes:
61
If differentiated using a 5-point quadratic Savitzky Golay method the peak-to-

peak measurement for the same functional form differs by 10%.
The FWHM used for the Gaussian is typical of an oxygen KLL peak. The scale
of the difference between peak-to-peak intensities for peaks of different
FWHM when measured using different step-sizes also varies. A peak-to-peak
intensity for a peak with FWHM 10 eV when measured using 1 eV and 0.5 eV
and differentiated using a 5-point Savitzky Golay method differs by 5%.
The RSFs in Briggs and Grant are specified for a 4 eV energy interval
numerical differentiation. In principle data acquired at 0.5 eV should
62
therefore be differentiated using a 9-point Savitzky Golay method, while data

acquired at 1 eV would require a 5-point Savitzky Golay differentiation. While
matching the number of points used in the Savitzky Golay method to the
step-size can improve the acquisition step-size dependency, the test peak of
FWHM 7 eV still results in a 1.8% difference in peak-to-peak height when
tabulated at 0.5 eV steps and differentiated with a 9-point quadratic Savitzky
Golay than when tabulated at 1 eV and differentiated with a 5-point
quadratic method.
Converting Direct Spectra to Differentiated Spectra

To convert a spectrum from direct form to differentiated form:
1. Display the spectrum in the active tile.
2. Invoke the Spectrum Processing dialog window and select the

Differentiation property page.
3. For data acquired using 1 eV step-size, select the SG Quadratic radio

button and enter 5 into the smoothing width text box.
63
4. Press the Apply button on the Differentiation property page.
An entry appears in the scrolled list on the Processing History property page.
Only the spectrum in the active tile is affected by the Differentiation property
page. When other spectra are included in the experiment and also require
differentiation, the processing performed on the spectrum in the active tile
can be propagated to data selected in the right-hand panes of the
experiment frame as follows:
1. Display a spectrum in the active tile for which the differentiation
operation is already performed and the Processing History property
page displays the text string for the differentiation instruction (e.g. Diff
SG D(2) P(5)).
64
2. Select the data blocks in the right-hand pane for which the
differentiation operation is also required.
3. Place the cursor over the active tile in the left-hand pane and invoke
the Browser Operations dialog window by right-click the mouse
button.
The Browser Operations dialog window lists those VAMAS blocks selected in
the right-hand pane of the experiment frame and offers a set of tick-boxes
which specify the type of information to be propagated from the VAMAS
65
block displayed in the active tile to the set of VAMAS blocks in the scrolled
list.
4. Check the list of selected VAMAS blocks on the dialog window and tick
the propagate Processing tick-box.
5. Press the OK button on the dialog window and confirm that the data
are now displayed as differentiated spectra.
Quantification Regions for AES data

Peak-to-peak intensities are measured using quantification regions.
Quantification regions specify:
1. The name for the region; also referred to as the quantification item
name.
2. The relative sensitivity factor, labelled RSF, for the peak intensity.
3. The energy interval over which the peak-to-peak intensity should be
determined.
66
Quantification regions are used for XPS data and therefore other fields such
as background type are also present on the Regions property page, but for
peak-to-peak measurements these other fields are of no importance.
The Quantification Parameters dialog window is available from the Options
menu or via the top toolbar.
A region is manually specified using the Regions property page on the

Quantification Parameters dialog window:
67
The name field in the quantification region is used to label the values
computed for the region in quantification reports.
Meaningful names improve the readability of quantification reports. Further,

the name field is used for manipulating intensities in the Custom Report used
for depth profiling experiments and therefore region names used in the
Custom Report should begin with an alphabetic character.
The peak-to-peak intensity is scaled using the RSF field on the Regions
property page.
The RSF is typically stored in the element library and retrieved using the
Element Library dialog window as described below.
The energy interval over which the peak-to-peak intensity is computed is
defined using two limits labelled start and end.
While the background type for peak-to-peak intensities is irrelevant from the
computational point of view, from a display perspective a background type of
zero provides a more meaningful reference than the typical XPS background
types.
68
Creating Quantification Regions using the Element Library

The advantage of creating quantification regions using the element library
lies in an explicit selection of the transition and therefore RSF appropriate for
the Auger peak. Regions are created using the Element Table property page.
The scrolled list on the Element Table property page combines with the
Regions property page on the Quantification Parameters dialog window to
create regions for the spectrum displayed in the active tile.
69
To create a region using the Element Table property page:

1. Display a spectrum in the active tile.
2. Invoke both the Quantification Parameters and Element Library dialog
windows.
3. Left-click the mouse with the cursor over the Auger peak in the left-
hand pane of the experiment frame. The table on the Element Table
property page scrolls to display those energies around the energy
indicated with the cursor and mouse.
4. Tick the box on the Element Table property page labelled Create When
Line Selected.
5. Ensure the Regions property page is top-most on the Quantification

Parameters dialog window.
6. Using the name field on the Element Table list, select the transition
corresponding to the data in the active tile.
A region is created with name and RSF assigned from the element library
entry selected.
70
7. Adjust the start and end for the quantification region by either
entering new values on the Regions property page or under mouse
control.
Propagation of Quantification Regions

A region defined on a spectrum can be propagated to other spectra for the
same transition. The propagation of regions is analogous with the
propagation of processing operations described above in the context of
differentiating a data set of many direct spectra.
To propagate a region:
1. Display the spectrum for which a region is defined in the active tile.
2. Select the set of VAMAS blocks in the right-hand pane to which the
region in the active tile is to be copied.
71
3. Right click the mouse with the cursor over the left-hand pane and
select the tick box labelled Regions in the Propagate section of the
Browser Operations dialog window.
4. Check that the scrolled list on the dialog window contains the intended
set of VAMAS blocks and press the OK button.
On completion, the set of spectra selected in the right-hand pane are

populated with copies of the region or regions defined on the spectrum in
the active tile.
Quantification Reports
Quantification reports are generated from those VAMAS blocks selected in
the right-hand pane of the experiment frame for which regions are defined.
The Report Spec property page on the Quantification Parameters dialog
72
window offers the two principal mechanisms by which quantification reports

are generated, namely, Standard Reports and Custom Reports.
The Report Spec property page offers the means of quantifying data acquired
as separate narrow scan spectra. The spectra used to quantify a surface
composition must be displayed in the same row as viewed via the right-hand
pane of the experiment frame.
The organisation of the VAMAS blocks in the right-hand pane is based on the
element (species)/transition VAMAS fields in the data blocks and the
experimental variable assigned to the VAMAS block. The values for these
VAMAS block parameters may be altered using several toolbar options.
73
The Edit VAMAS fields dialog window acts on the data displayed in the active
tile. Other dialog windows act on selections in the right-hand pane.
VAMAS blocks with the same element/transition fields appear in the same
column in the right-hand pane, while VAMAS blocks with the same
experimental variable appear, where possible, in the same row.
74
Standard Reports
Standard reports are configurable row-orientated reports generated from
survey and/or narrow scan spectra measured from the same surface.
Creating a quantification report involves:
1. Creating quantification regions for each peak used to characterise the
sample.
2. Selecting in the right-hand pane the VAMAS blocks containing the
spectra for which regions are defined.
75
3. Invoking the Quantification Parameters dialog window and selecting

the Report Spec property page.
4. Pressing the button labelled Regions in the Standard Report Section on
the Report Spec property page.
When the Regions button is pressed, if the Use Config File tick-box is ticked a
configuration file is used to define the information appearing in the text
report. A detailed discussion regarding these configuration files is presented
in a later section. The report generated from one specific configuration file
appears as a text report in CasaXPS.
A quantification report generated from the standard report options is copied

through the clipboard by pressing the Copy toolbar button or Control-C at the
time the text report window has focus in CasaXPS.
76
Any program capable of accepting text via the clipboard can be used to
further manipulate the data. The data placed on the clipboard includes a
variety of tabulation formats, not all applicable to peak-to-peak data.
Configuration Files for Standard Reports

The configuration files for the standard report are constructed from a set of
keywords entered into an ASCII file one keyword per line. The keywords are:
Keyword Description
VARIABLE Experimental Variable value from the VAMAS block or Row Label when in Edit Mode
NAME Region or component name.

POSITION Peak position.
FWHM Peak full width at half maximum
AREA Peak area correct for transmission and energy dependence but not RSF
RSF Relative Sensitivity Factor
CONCENTRATION % Atomic Concentration
ERROR_BAR Std Deviation in % atomic concentration for regions
START Quantification region lower limit
END Quantification region upper limit
Intensity for peak to peak Auger Peak intensity maximum to minimum
PEAK_TO_PEAK
XPS/SIMS peak height above background
PEAK_TO_PEAK_CONC % Concentration measured using peak to peak intensity
LINE_SHAPE Synthetic line-shape for a component
AREA_ERROR_BAR Std Deviation in peak area measured using a quantification region.
TRANSITION_TAG Tag string from region or component
POSITION_CONST Component position constraint string
AREA_CONST Component area constraint string
FWHM_CONST Component FWHM constraint string
77
Column character appearing above a region or component on the respective property

COLUMN_LABEL
page
DEGREES_OF_FREEDOM Degrees of freedom used to compute the figure of merit from least squares fit.
VAMAS_BLOCK_NAME VAMAS block identifier
CENTROID Position of the centroid of a peak
MASS Mass assigned to a region or component
MASS_CONC % Mass Concentration
SIGNAL_TO_NOISE Std Dev for noise distribution
CORRECTED_AREA Peak area corrected by the total sensitivity factor
TOTAL_SENSITIVITY_FACTOR Combined factor from RSF, Transmission and energy dependence factors
TRANSMISSION Transmission function value at peak maximum
MEAN_FREE_PATH Kinetic energy dependence factor
RAW_AREA Uncorrected integral of background subtracted signal
PEAK_PLUS Peak intensity above background
PEAK_MINUS Peak intensity below background
SIMS_PEAK_AREA Summation of data channel
VAMAS_BLOCK_SAMPLE_ID VAMAS Sample Identifier string
Notepad or any other means of creating an ASCII file can be employed to

create the configuration files.
The configuration file used to generate the standard report is located on the
disk relative to the directory containing the CasaXPS.exe executable file.
Within the same directory as the CasaXPS.exe executable file is a directory
called CasaXPS.DEF. Default settings enabled on starting a new CasaXPS
session are also saved in the CasaXPS.DEF directory.
Each type of configuration file for the standard report options is identified by
key names; specifically, the file called RegionQuantTable.txt provides the
configuration information for the columns in the standard report generated
when the Regions button in the standard report section is pressed. Similarly,
other configuration files with key names are associated with the other
reporting options in the standard report section. These configuration files are
used by default each time a standard report is requested and are most
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appropriate for those users requiring a fixed format for each report
generated.
A further feature allows a choice of configuration files. If a directory exists in
the CasaXPS.DEF directory by the name of QuantTables, then on pressing a
standard report button the user is offered a list of configuration file. The
report format is dependent on the choice made from the list.
Since all files in the directory CasaXPS.DEF/QuantTables are offered in the

dialog window, the names of the files within the QuantTables directory are
unimportant and therefore the correct configuration file for the type of data
must be selected.
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To quantify the Auger survey:

Select in the right-hand pane the VAMAS block containing the AES survey
spectrum and press the Regions button from the Standard Report section.
On the resulting dialog window, select the configuration file from the list and
press the Select button. The quantification table appears with column
headings defined by the configuration file.
A different report is obtained from a similar sequence of steps for the XPS
survey spectrum recorded from the same sample and located in the same
VAMAS file. By selecting the configuration file prepared for XPS data an
appropriate report is selectively produced; XPS spectra are typically
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quantified using peak area after background subtraction rather than the
peak-to-peak approach of Auger spectra.
In the event no selection is made from the dialog window invoked by

pressing the Regions button, the default configuration file for the Regions
button is used to generate the report. The default configuration file for the
Regions button on the Standard report is located in the CasaXPS.DEF
directory with the key name RegionQuantTable.txt.
The selection dialog window only appears if the QuantTables directory exists
in the CasaXPS.DEF directory. The default configuration file for the Regions
button is automatically used if the CasaXPS.DEF directory is prepared without
the QuantTables subdirectory.
Custom Reports
Custom reports are not configurable and data are presented in columns with
each row of the table associated with an experimental variable. The intention
is to provide a means of profiling changes in spectra with respect to etch time
or angle or any parameter that varies through the course of an experiment.
The Custom Report, like the Standard Report, only applies to the current
selection in the right-hand pane of the experiment frame. Regions and
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components are treated identically within the custom report and are referred
to as quantification items, where both forms of these quantification items
are identified by the name fields used in the definition of the regions and
components. When a VAMAS block is selected in the right-hand pane, all the
region names and component names are collected into a list displayed under
the heading Quantification Item Names.
Only quantification item names appearing in the Quantification Item Names

list are used in the custom report.
A custom report is defined in terms of the currently active quantification item

names using the Name and Formula table.
The Names and Formula table can be initially populated using the set of
buttons between the two tables. Pressing the Regions button between the
Quantification Item Names table and the Names and Formula table causes
the set of unique region names currently displayed in the Quantification Item
Names table to be transferred to the Names and Formula table. The Names
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and Formula entries can be edited by right-clicking the mouse with the cursor
over a name entry in the lower table.
The function of the buttons between the two tables is to provide an initial
state for the Names and Formula table. Although the action apparently loads
the Names and Formula table using information from Regions, for example, it
is important to note that any component with the same name as a region will
also be included in the custom quantification report regardless of whether
the Region button was initially pressed. The objective for the custom report is
to provide a flexible means of combining intensities from both regions and
components, so to differentiate between regions and components different
name should be used.
A further word of warning is that any quantification item with identical
names will be summed together. This feature makes it doubly important that
regions and components should be assigned different names. The
consequence of not using unique names for regions and components is the
intensities will effectively be doubled for any spectrum for which a region
defines the background for a component. Peak fitting with components is
rarely performed for Auger spectra, so this warning is less important for
Auger as for those using XPS, but nevertheless, custom reports will sum
regions with identical names therefore an awareness of the mechanism is
important.
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For the purposes of profiling the data being used as an example, initially a
custom report simply based on the region names is sufficient. To create the
Names and Formula entries:
1. Select the VAMAS blocks containing the quantification regions
previously prepared.
2. Press the Regions button between the two tables in the custom report
section.
3. Since the data are in derivative form and therefore peak-to-peak

intensities and RSFs are in use, press the Height Report button in the
custom report section.
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The resulting quantification table represents two sets of traces, namely, a set
of corrected peak intensities in CPS and a set of atomic concentrations
expressed as a percentage. These data may be placed on the clipboard using
the Copy toolbar button (or Control-C) and pasted into plotting software or
further manipulated in CasaXPS. A VAMAS view of the profiles is obtained
either as a separate VAMAS file or within the current spectrum file using the
File menu offered while the report window has focus.
The Create Profile menu option causes a new experiment frame to appear
containing two rows of VAMAS blocks. The top row corresponds to the
atomic percentage columns in the quantification report, while the second
row in the new experiment frame corresponds to the RSF corrected peak-to-
peak intensities.
The second option for displaying the profile data allows the features in the
profile to be correlated with the spectra from which the profile is derived.
Selecting the Add Profile menu option from the File menu causes the profile
data to be added to the original VAMAS file containing the spectra. When a
profile is added to the spectral data, a string is added to the display of the
spectra in the active tile.
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The string Ctrl+F8 Profile indicates that holding down the Control key on the
keyboard and pressing the F8 function key cause the display to switch from
spectra to the most recently added profile data.
Crtl+F8
A raw Auger depth profile may therefore be viewed in spectrum format,

where rows of spectra ordered with respect to etch-time, and processed
profile format, where traces computed from the spectra are plotted against
etch-time. The Control+F8 key stroke not only switches between the two
perspectives of the data, but also changes the display of the spectra based on
the position of the cursor when viewed in profile format, or the displayed
position of the cursor in the profile format based on the selection in the
right-hand pane when viewed in spectrum format. The row currently selected
in the spectrum format of the profile, and therefore the etch time, translates
into to position of the cursor on the profile format of the data. Similarly, a
cursor placed on the profile format of the data becomes a selected row of
spectra when the Control+F8 action is pressed causing the display to revert
back to the spectrum format.
It is also possible to indicate a range of spectra via the normal selection
mechanism in the right-hand pane of the experiment frame displaying the
spectra. On pressing Ctrl+F8, a pair of vertical cursors indicates where in the
profile the selected spectra correspond in the profile. Again, if a pair of
vertical cursors is placed on the profile trace, on switching back to the
spectrum form of the data, the range of spectra indicated by the cursors on
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the profile becomes selected in the right-hand pane of the spectrum form of
the data.
Crtl+F8
To mark the profile with a pair of cursors, hold the Shift key down while
dragging the cursor across the active tile displaying the profile. On releasing
the mouse button, the drag box marks the position of the two cursors.
An Advanced use of the Custom Report

The profile used to illustrate the custom report involves erbium and
molybdenum. The basic profile created using region intensities suggests a
correlation between the molybdenum layer and the erbium surface layer.
Since the erbium Auger peak used in the profile is located near a
molybdenum peak, examining the intensity of the erbium will require a more
detailed analysis than simply following the profiles of region intensities.
Examining the direct spectra at etch-times close to the molybdenum
interface confirms the influence of the molybdenum Auger line on the
intensity measured for erbium.
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It is therefore proposed to calculate the erbium intensity using the

molybdenum region to remove the molybdenum peak-to-peak intensity
contribution from the erbium region. To estimate the relationship between
the peak-to-peak intensity for the molybdenum interference and the Mo1
Auger transition, a representative pair of spectra is selected and used to
measure the intensity ratio of the Er1 region to the Mo1 region, where it is
assumed the Er1 region is at a point in the profile such that the erbium signal
is negligible compared to molybdenum.
Measuring the ratio of these molybdenum peaks can be performed using the
custom report:
1. Select the two VAMAS blocks containing the erbium and molybdenum
data for an etch-time where erbium is not significant.
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2. Select the Mo1 name in the Quantification Item Names table on the
Custom Report section of the Report Spec property page before
pressing the Ratio Region button.
The Names and Formula table is populated with formulae involving a simple
division with respect to the Mo1 quantification items selected in the table
above. Pressing the Height Report button followed by the Copy toolbar
button results in a dialog window from which the ratio can be selected,
copied, and then pasted into a new set of formulae for profiling the full
experiment.
To profile the full experiment:

1. Select all the VAMAS blocks for which regions are defined.
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2. Press the Regions button between the Quantification Item Names

table and the Names and Formula table.
3. Right-click with the cursor over the name field for the Er1 entry in the
Names and Formula table.
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4. Enter the formula for the modification to the erbium intensity based
on the ratio previously determined.
5. Press the Height Report button on the Custom Report Section.
The custom report table can again be exported using the Copy toolbar
button, or a VAMAS form of the profile can be created using the File menu.
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Ideally, the relative intensity of the Mo1 peak to the molybdenum peak
measured at the same energy as the erbium should have been measured
using a molybdenum standard rather than assuming a value computed from
the profile data.
An alternative to manipulating the peak intensities via the custom report is to
use a least squares approach to separate the erbium from molybdenum
interference.
Least Squares Approach to Depth Profile Interpretation

A least squares procedure offers a means of partitioning a spectrum into
component spectra. The component spectra are chosen to embody the
transitions responsible for the measured data. Once these component
spectra are determined in a least squares sense, the relative contributions of
these underlying transitions to the measured data can be identified using
quantification regions in exactly the same way any spectrum in the profile is
quantified.
The least squares procedure is described in the context of the Savitzky Golay
algorithm for differentiating the Auger direct spectra. The essential
difference in the least squares decomposition of spectra compared to the
Savitzky Golay algorithm is the basis functions are now spectra rather than
terms (1, x, x2, ...) in a polynomial. The net result is the same in the sense that
a spectrum s is expressed as a linear combination of a set of n component
spectra ci.
The coefficients ai are determined in a least squares sense and the spectrum
s is therefore decomposed into component spectra aici.
By way of example, the erbium/molybdenum problem will now be addressed
using a least squares decomposition.
Least Squares Example

While the data in the Auger depth profile will be quantified using the
differentiated spectra, since the act of differentiation involves a Savitzky-
Golay operation which effectively smoothes the data, the least squares
analysis will be performed on the raw direct spectra rather than working with
already processed differentiated data.
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The first step is to identify the component spectra for use in the least squares
decomposition. Overlaying the Er1 VAMAS blocks in the active tile offers an
easy partition of the data into three forms: pure erbium, predominantly
molybdenum, and background signal measured at depths below either the
erbium and molybdenum layers.
In general it is good practice to improve the signal to noise ratio in the

component spectra by adding together appropriate sets of spectra from the
three zones identified. While the Calculator property page on the Spectrum
Processing dialog window provides a means of combining spectra acquired
under varying conditions, the data from the depth profile are very uniform in
the acquisition parameters; therefore, summing a set of spectra such as
these is achieved in a simple fashion using the Test Data property page on
the Spectrum processing dialog window.
The Test Data dialog window offers a range of miscellaneous processing
options, two of which permit data to be summed without regard to
acquisition conditions. That is, these options are only appropriate for very
specific cases in which all the spectra have identical numbers of data
channels. To sum data from a set of VAMAS blocks:
1. Select an appropriate set of spectra over which a summation can be
performed.
2. Invoke the Spectrum Processing Dialog window and select the Test
Data property page.
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3. Overlay the selected VAMAS blocks in the active tile.
4. Press the SUM button on the Test data property page.
Note: the SUM All button should not be used as the SUM All button includes
each corresponding variable in each VAMAS block in the summation. Most
spectra include transmission function information as a corresponding
variable; therefore, the resulting spectrum would be incorrect if the SUM All
button were used. The SUM All button is used for imaging data sets where
spectra-at-pixels appear in the VAMAS file as corresponding variables in
VAMAS blocks.
Following the use of the SUM button acting on the spectra overlaid in the
active tile, a new VAMAS block appears in the right-hand pane which
contains the sum of the spectra appearing in the active tile.
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For the current example where three zones within the profile are identified,
the summation steps need to be repeated for the molybdenum layers and
also the layers beneath both the erbium and molybdenum layers. The
resulting experiment frame now contains three additional VAMAS blocks
appended to the column headed Er1. Adjusting the VAMAS block identifiers
for these three summed spectra helps to understand the context of these
data in the experiment frame created by the linear least squares procedure.
The toolbar option for editing the block identifier applies to the VAMAS
blocks selected in the right-hand pane.
Having created the three component spectra, select and overlay the
component spectra in the active tile.
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The component spectra overlaid in the active tile are used to fit the spectra
selected in the right-hand pane. To create an experiment frame containing
the least squares decomposition of the erbium spectra:
1. Select the column of erbium spectra.
2. Invoke the Spectrum Processing dialog window and select the PCA
property page.
3. Press the Generate Spectra button in the Linear Analysis section of the
property page.
A new experiment frame opens containing a row for each VAMAS block
selected in the original experiment frame containing the depth profile. Each
row includes the original VAMAS block followed by the least squares
approximation to the original spectrum based on the component spectra,
followed by each scaled component spectrum.
In order to profile the erbium signal, the column in the new experiment
frame corresponding to the scaled erbium component from the least squares
decomposition must be copied back to the original depth profile experiment
frame. Once the erbium component is returned to the originating data file,
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the profiling steps can be followed where the unprocessed erbium spectra
are replaced in the profile by the new least squares component data.
To copy the erbium components:
1. Select the column of VAMAS blocks representing the erbium
component spectra.
2. Switch focus to the original experiment frame and press the

Copy/Paste toolbar button.
The VAMAS blocks corresponding to the components are now moved to the
original experiment frame.
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Since the component erbium spectra represent the contribution of the

erbium only, the profile is now performed as before based on simple regions
where the component spectra replace the role of the raw erbium spectra.
That is, the component spectra require differentiating and a region created
for the Er1 transition before the profiling steps are repeated for the file. The
raw Er1 spectra are not included but are substituted by the component
spectra.
The profile created by this method also removes the apparent correlation
previously obtained by the basic analysis of the profile with simple regions.
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Linear Least Squares

While the linear least squares approach is a powerful tool when used
correctly, the least squares criterion may produce poor representations of
the original spectra due to an incomplete set of component spectra. For this
reason, the results of a linear least squares decomposition are offered in a
new experiment frame with the view to assessing the validity of the
decomposition. Overlaying the raw spectrum together with the least squares
solutions provides a visual feedback of how well the procedure applied to the
profile data.
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A useful option for displaying the spectra generated from the least squares
procedure is the Tile by Row toolbar button.
Selecting a set of rows in the right-hand pane before pressing the toolbar
button causes the creation of one display tile per row of selected VAMAS
blocks in the right-hand pane where each tile appearing in the left-hand pane
displays an overlay of spectra from a row of selected VAMAS blocks.
CasaXPS Element Library

Elemental identification and quantification using XPS/AES spectra rely on the
maintenance of libraries containing peak positions and relative sensitivity
factors. The default CasaXPS element library is compiled using rough peak
positions and Scofield cross-sections for aluminium and magnesium X-ray
anodes to represent the corresponding relative sensitivity of the
photoelectric peaks relative to the C 1s transition. While appropriate for
some, these peak energies and relative sensitivity factors will not satisfy all
and therefore the CasaXPS system offers mechanisms for user, technique and
sample specific element library creation. This section describes the means for
modifying the element library in CasaXPS.
Element Library Format

The CasaXPS element library is an ASCII file. The first line in the file is a
version number, which may be 0, 1 or 2. Library files updated from version
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2.3.15 of CasaXPS are written in version 2 format. The format for version 1
and version 2 files is TAB spaced ASCII organised so that the data are easily
edited in a spreadsheet program such as Excel. The difference between
version 2 and version 1 formatted files is simply the ability of the version 2
format to include additional user-defined TAB spaced fields appended to the
end of the standard set of fields defined for version 1 library files. Each entry
within an element library file consists of the following standard fields:
1. Element
2. Transition
3. Label/Name
4. Mass (Daltons)
5. Energy Type (BE or KE)
6. Energy (eV)
7. F.W.H.M.
8. Line shape (e.g. GL(30))
9. Relative Sensitivity Factor
10.Excitation source string
These standard fields when viewed via a spreadsheet appear as follows:
For a large number of changes, using a spreadsheet is the best means of

constructing a CasaXPS library; however, for small alterations the Element
Library property page offers dialog-window-based adjustments of the library.
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Note how the library entries visible in the spreadsheet include two different
excitation source strings, namely Al and Mg. A single library file may contain
any number of entries corresponding to different excitation source strings;
however, when used in CasaXPS these strings are matched to the excitation
source string in the displayed VAMAS block in the active tile. Only those
library entries for which a match occurs are displayed on the Element Table
property page of the Element Library dialog window. Thus, an XPS spectrum
displayed in the active tile measured with an Al anode, and therefore
assigned a source label of Al, will cause the Element Table property page to
list only those element library entries with matching excitation strings.
The transitions listed because of a match between the excitation source
string and the VAMAS block source label field are supplemented by
transitions with excitation source entries identified using the string Any.
These additional element library entries with excitation source string Any are
for XPS induced Auger transitions, the function of which is to simply mark the
position of Auger lines in any XPS spectrum. Since these Auger lines do not
specify lines used in quantification, the RSF for these Auger lines is typically
zero. An XPS induced Auger line for which an RSF has been established may
be entered into the library using an Energy Type of KE and excitation source
string appropriate for the data.
The element table offered for the XPS spectrum should be compared to the
entries displayed from the same element library file when the data in the
active tile is an Auger spectrum.
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The transitions offered in the element table are specific to the Auger data in
the active tile. When the Source Label field for the data includes the string
electron gun, the string used to match the entries in the element library is
constructed from the electron gun energy parameter in the VAMAS block.
Hence, in the current example data, since the electron gun energy is 3000 eV,
the string used to display the Auger transitions in the element table is S(3).
Although version 2 of the library format is aimed at editing library files within
a spreadsheet program, a mechanism exits within CasaXPS for making
occasional changes and additions to the currently loaded library file. The Edit
Entry dialog window is invoked by placing the cursor over the Name field for
an entry in the element table before right-clicking the mouse button. The
current set of library fields for the selected peak is displayed on the dialog
window. These fields can be adjusted, then either updated or a new entry
created.
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The Edit Entry dialog window allows the library entry to be altered and then
updated using the OK button. Alternatively, pressing the Create button
causes a new library entry to be added to the element library based on the
parameters defined on the dialog window. The Delete button will remove the
entry used to invoke the dialog window.
Any modifications to the element library within CasaXPS are only written
back to disk once the current session of CasaXPS is ended. On exiting
CasaXPS, a File dialog window presents the opportunity to save the changes
to a new filename.
On starting CasaXPS, the library file CasaXPS.lib located in the same directory
as the executable file CasaXPS.exe is loaded as the default element library. In
general, when a spectrum is displayed in the active tile, on invoking the
Element library dialog window, the Element Table property page displays
those entries for which the excitation source string from the entry matches
the corresponding field in the VAMAS block holding the spectrum. The
exception to this rule occurs for AES data. If the excitation source field in the
VAMAS block is set to a string including the key words electron and gun, then
for Auger spectra the electron gun energy is used to construct the string used
to match an excitation source in the element library. For example, an AES
element library might include relative sensitivity factors for electron beam
energies 3 keV, 5 keV and 10 keV, and therefore should have entries with
excitation source strings S(3), S(5) and S(10).
A set of sensitivity factors for AES are published in the book edited by Briggs
and Grant (ISBN 1 901019 047); different instrument manufacturers
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recommend different sensitivity factors for specific instruments, so an

appropriate library for a given instrument should be prepared.
Importing a JEOL Element Library

A file format used by JEOL Auger instruments is supported in CasaXPS as a
means of importing transition and RSF information into the CasaXPS element
library. The file format is a relatively simple format.
Importing these files into CasaXPS involves the Input File property page on
the Element Library dialog window.
To import a JEOL formatted file:

1. Using the File dialog invoked by the Browse button, browse for the
ASCII file. Select the file and press the Open button on the File dialog.
The selected file is entered onto the Input File property page.
2. Select the radio button labelled JEOL AES.
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3. Enter the information into the element library by pressing either the
Load button to overwrite the existing element library or Merge button
to add the new entries to the current element library.
The JEOL library files include an entry specifying the electron gun energy;
therefore a JOEL formatted file is required for each electron-gun energy. In
addition, the JEOL library files are either for differentiated spectra peak-to-
peak measurements or direct spectra measurements. The two different files
contain different RSF values depending on the type of spectra analysed
during quantification.
Concentration Calculation
The principal means of comparing XPS/AES samples in CasaXPS is via
percentage concentration values. The names assigned to these quantities are
an indication of the source for the values rather than an assertion that the
tables necessarily contain atomic or mass concentration for the surface
material. The accuracy of these concentration values depends on appropriate
transition and instrumental specific corrections as well as matrix context for
the material analysed. The objective in using concentration values to
characterise a sample is to reduce the intensity values to a set of normalised
quantities in the hope that some of the measurement artefacts are removed
from consideration when different samples are compared.
A concentration calculation consists of determining intensities for the
transitions computed from the raw data , followed by a correction based on
the transition, encapsulated in the RSF and, where available transmission
correction accommodating instrumental intensity variations. The
concentration for an element is given by
The intensity may be measured using peak height above background, peak-
to-peak or peak area. For mass concentration the raw intensity is multiplied
by the mass for the element. The essential feature for these quantities is the
normalisation to the total signal measured.
While the standard method for measuring intensity for Auger spectra is
based on peak maximum to peak minimum (peak-to-peak) within a
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quantification region, other methods are possible within CasaXPS. Extracting

these alternative intensity values is dependent on the background type used
within the quantification region.
To reveal the set of possible background types, hold the Control Key down
and left-click the mouse with the cursor over a background type string on the
Regions property page of the Quantification Parameters dialog window.
The alternative methods from peak-to-peak for computing peak intensities

are for spectra in direct mode:
1. Peak height above background, where the background intensity is
measured at the left hand side of the quantification region.
2. Peak height above background, where the background intensity is
measured at the right hand side of the quantification region.
3. The ratio of the Peak height above background to the background
intensity.
The background types corresponding to these options are Height Left, Height
Right and (P-B)/B.
Height Right:
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Height Left:
(P-B)/B:
The ratio of peak height above background divided by the background

intensity is a means of normalising the peak intensities with respect to
background variations. These ratios are sometimes referred to as
topographical corrections when used in the context of imaging where peak
and background images are measured. Imaging Auger instruments without
hardware signal differentiation necessarily measure images in direct mode
and therefore these intensity measures provide insight into the quantities
exploited by imaging instruments.
Auger Imaging in CasaXPS

The electron gun technology required for Auger spectroscopy is also capable
of generating spatially monitored Auger signal and therefore Auger imaging is
often included as an option. Submicron spatial resolution requires vibration
isolation and screening of stray electromagnetic fields within the analysis
chamber to allow precise scanning Auger microscopy (SAM). Not all Auger
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instruments include such additional engineering, but nevertheless imaging is

a natural feature of Auger systems.
Auger images, when measured at a peak maximum are often difficult to

interpret. Fluctuations in the signal as a function of position on the sample
causes variation in the pixel intensities independent of the chemical
information desired from the surface of the material. The difficulty arises
because Auger images are typically collected in direct mode at the peak
maximum and unlike spectral measurements, are often taken in isolation;
background variations are sufficient to hamper the interpretation of such
images. In an attempt to reduce these effects, images are often also acquired
at an energy representative of the background and sometimes at a second
background energy, with the view to including a contribution from the
background to the final image and thereby improving the estimate of the
peak height at each pixel. A common calculation for an Auger analysis is the,
so called, topographical correction computed from the peak maximum N1
and a background image N2, namely (N1-N2) / N2. A variation on a theme is to
compute an image from (N1-N2) / (N1+N2).
The principal reason for analysing Auger images using peak and background
intensities is the time constraint of doing more; however, the benefits of
applying spectroscopic techniques to image analysis may, when possible, out
weigh the time penalty of performing the extended acquisitions of images
and allow spectra at each pixel to be determined. The example examined
below (data provided by Pennsylvania State University, USA), is a simple
experiment in which a gold grid is placed over a clean silver surface, and a set
of Auger images are acquired at unit eV step size across a silver Auger peak.
As luck would have it, a weak gold Auger line is also included in the energy
range over which the images were recorded and therefore the data set offers
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a means of illustrating a simple, yet effective procedure for creating

elemental Auger images. Viewing the full set of images in the raw direct
mode intensity leaves the impression that the grid is silver rather than gold.
Rather than using the direct spectra, following the conventional wisdom for
Auger spectra, the data are differentiated and peak-to-peak measurements
made for each pixel in the image. Simple quantification regions are defined
on the spectra, one for the silver Auger line and one for the weak gold Auger
line.
Two images of the peak-to-peak intensities are constructed; these two

images in turn are quantified using the standard procedure for quantifying
spectra.
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The results are two images, where the silver image is free from intensity
variations other than the elemental surface composition. A comparison with
an image obtained from a topographically corrected intensity shows how the
normalisation to the total intensity for both Ag and Au regions eliminates to a
greater extent the shadowing from the gold grid on the silver.
Regardless of which of the three methods are used to process the raw Auger
images, the most striking point is all three methods recover the true
composition of the grid, namely, gold rather than silver.
In many ways, the improved quality of the gold and silver images are
reassuring, since for years it has been assumed Auger spectra taken from a
single point on a sample can be compared by determining atomic
concentrations from the relative intensities of differentiated Auger peaks.
The images were determined from the peak-to-peak intensities without
application of relative sensitivity factors, however provided the appropriate
data are available, proper atomic concentration images are possible and
these images allow the surface to be viewed using the same regime normally
adopted for spectra.
Auger Image Analysis Steps in CasaXPS

The essential sequence of steps required to process the image data is as
follows:
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1. Convert the image set to spectra at each pixel.

2. Differentiate all the spectra.
3. Define quantification regions for each transition and propagate
these quantification regions to each VAMAS block containing a row
of spectra.
4. Convert the region intensities to images.
Within these steps there are potentially sub-steps and these sub-steps are
detailed below based on the original data for the given example.
The Auger images were acquired on a PHI Auger system, in this particular
case, using two data files in which the saved images correspond to a
sequence of unit energy steps over an interval spanning 370 eV to 331 eV.
Since the data are in two separate files, the first job after the data are
converted to VAMAS format is to assign the correct energy to the
experimental variable for each image and then move the images into a new
experiment frame.
Ordering the Images using the Experimental Variable

Initially, when converted through CasaXPS, the PHI .map files each contain
half the images for the entire data set. The images are assigned the same
experimental variable and the species/transition VAMAS block fields are all
different, therefore the VAMAS blocks appear in the right-hand pane of the
experiment frame as a single row.
To convert a set of images to spectra at each pixel, the images must appear
in the same column and the experimental variable for each image assigned
the value for the energy at which the image was acquired. To reorganize the
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data as required, the next step is to assign the species/transition fields for
each VAMAS block in the file:
1. Select the entire set of VAMAS block in the Experiment Frame.
Since the data blocks appear in a single row in the right-hand pane, the entire
set of blocks are selected by either left-clicking the mouse with the cursor
over experimental variable value; or click once on the button heading the
column for the experimental variable values. Both these actions will result in
the full set of VAMAS blocks being selected. The former action relies on all
the data appearing in a single row, whereas the latter selects the entire set of
VAMAS blocks in the experiment frame.
2. Press the button on the second toolbar and enter new
Element/Transition strings on the resulting dialog window. When the
OK button is pressed, all the selected VAMAS blocks are assigned the
pair of strings entered on the dialog window and as a consequence, the
right-hand-side of the Experiment Frame is reordered so that all the
VAMAS blocks appear in a single column.
Once the VAMAS blocks appear as a single column in the right-hand pane of
the experiment frame, the values for the experimental variable can be
adjusted to the energy at which each image was acquired. The two toolbar
buttons provide a means of assigning the experimental variable value
on bulk; however the left-most of this pair of buttons offers a means of
specifying a range of values for the experimental variable, where each row of
VAMAS blocks will be assigned intermediate values. Thus, following
rearrangement into a single column, the VAMAS blocks are assigned the
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appropriate experimental variable values by specifying the range 370 ʹ 351

eV.
Similarly the second file can be adjusted into a column of VAMAS blocks by
assigning the same element/transition strings to each VAMAS block used in
the first file and reassigning the experimental variables for the images using
the toolbar button to specify the range 350 ʹ 331 eV. After making these
assignments for the experimental values to both files, the two sets of VAMAS
blocks can be merged into a new experiment frame.
Copying VAMAS blocks between Experiment Frames

Moving VAMAS blocks between experiment frames involves selecting in the
right-hand panes all those blocks to be copied, transferring focus to the
destination experiment frame before pressing the Copy/Paste VAMAS blocks
toolbar button .
On pressing the toolbar button a dialog window listing all the selected
VAMAS blocks provides a means of checking only the intended blocks are
selected.
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The OK button on the dialog window accepts the selection and results in
copies of the selected blocks being merged into the experiment frame with
focus.
Although the VAMAS blocks now appear in the same experiment frame all in
one column and the map energy is assigned to the experimental variable,
there is still one possible problem. The images are ordered from high kinetic
energy to low and so the spectra, when generated, will be assumed to be XPS
data rather than AES. It is also possible that the merged files appear back to
front, from the energy scale perspective, and so the true order of the images,
with respect to energy, may yet be realized. The functionality in the second
button for assigning the experimental value is required to force the
appropriate reordering. The dialog window invoked by the right of the
two toolbar buttons allows the assignment of the experimental variable for a
selected set of VAMAS blocks.
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Further, once the assignment for the selection is made, the VAMAS blocks
are reordered with respect to the new set of experimental variables. To
cause a reordering of the image set, simply select a single VAMAS block and
press the OK button on the dialog window. Although no new value was
actually assigned, the reordering will still take place and the images then
appear in the experiment frame ordered with respect to the map energies.
Converting Images to Differentiated Spectra

Given the set of images, now ordered with respect to energy, the analysis
proceeds by converting the image data set into a set of spectra, one
spectrum per image pixel. The conversion from images to spectra is achieved
using the Image Processing property page on the Image Processing dialog
window.
To invoke the Image Processing dialog window, click on the displayed image
to ensure the Options menu items are active, and then select the Image
Processing menu option. Overlay the images in the Active Tile and press the
Convert Images to Spectra button on the Image Processing property page.
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It is important that all the images are acquired using the same acquisition
time and the experimental variable represents a sequence of evenly spaced
energies. If the step in energy between the images deviates from a constant
difference, then an error message will appear and no conversion to spectra
takes place.
The converted spectra appear in a new experiment frame, where the
experimental variable is labelled pixel and the values for the experimental
variables represent row indices of the pixels in the original images.
Each VAMAS block contains an entire row of spectra; the spectra are stored
as corresponding variables in each VAMAS block and as a result of the
method used to store the spectra at pixels, a new processing option on the
Differentiation property page of the Spectrum Processing dialog window
specifies that the operation should be applied to all the corresponding
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variables in a VAMAS block, rather than simply to the corresponding variable

currently displayed in the active tile.
The data in all the VAMAS blocks must be differentiated. Therefore once the
data in the active tile is differentiated, the propagate mechanism should be
used to process all the VAMAS blocks similarly.
To propagate the differentiation, select the entire set of VAMAS blocks in the
right-hand pane of the experiment frame and right-click the mouse button
over the active tile containing the differentiated spectrum.
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On the Browser Operations dialog window, tick the Processing tick-box within
the Propagate section and press the OK button. All the spectra within the
targeted VAMAS blocks will be differentiated.
Since the spectra generated from images are stored as multiple

corresponding variables and only one corresponding variable from a given
VAMAS block can be viewed at a time, it becomes necessary to step through
the corresponding variables to inspect the results of the differentiation
operation. To step through the corresponding variables in a VAMAS block,
the Control + Page-Up and Control + Page-Down keyboard buttons are used.
The corresponding variable index in each VAMAS block within an experiment
frame is adjusted by the Control + Page-Up and Control + Page-Down keys.
Similarly, Control + Home and Control + End move the corresponding variable
index to the beginning and end indices for each VAMAS block in the
experiment frame. To adjust the index for a corresponding variable on a
VAMAS block by VAMAS block basis, using the Page-Up, Page-Down, Home
and End keyboard keys whilst holding down the Shift key causes only the
VAMAS blocks in the active tile to be adjusted.
Quantifying the Spectra at Pixels to Produce Images

The quantification of Auger spectra is typically performed using the peak-to-
peak metric to measure line intensity. In this example, two Auger lines are
evident in the energy range 331 ʹ 370 eV and so two quantification regions
can be defined on each spectrum as indicated by the grey bands over the
data.
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These quantification regions are defined on the Quantification Parameters

dialog window via the Regions property page. The regions for use with the
spectra-to-images options are identical to those used for general spectral
quantification, but with one slight difference. The default action of the
Convert Regions to Images button on the Image Processing property page is
to create images using the integrated intensity based on peak area. For
differentiated AES data, the peak-to-peak intensity is required; therefore to
create images appropriate for the differentiated data, the Tag field in the
region specification table must be assigned a keyword string, namely, peak to
peak.
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The Tag field is also used to switch between other parameters determined
from regions such as fwhm, position and centroid; using these various region
outputs, the surface mapped by the images can be viewed with respect to
peak broadening or peak shifts. Again the Tag field is entered with the
appropriate keyword string e.g. fwhm, position or centroid.
Once quantification regions have been propagated to each VAMAS block in
the spectrum file, the corresponding images are generated by overlaying all
the spectra from the VAMAS blocks in the active tile and pressing the Convert
Regions to Images button on the Image Processing property page.
Ideally, images for each element identifiable on the sample surface should be
measures and a similar analysis to the Ag and Au data performed for each
element. In this example only two elemental images were recorded, but
nevertheless, proceeding to the quantification step based on the two
available images has merit in that the resulting images are normalized with
respect to each other across the field of view.
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The button labelled Quantify Images can be used to perform the operation.
The calculation assumes the images are generated from either quantification
regions or synthetic components, both of which are in units of CPSeV (for
area based intensities) or CPS (for peak-to-peak measurements), therefore
the new images are generated simply using the formula Ij / (I0+I1н ͙ н/n).
Intensity adjustments for relative sensitivity are accommodated by entering
an appropriate value in the RSF field in the quantification regions or
components. To perform the quantification step, overlay all the images in the
active tile, then press the Quantify Images button. A new experiment frame is
created containing the quantified images.
Note, a second button labelled Quantify Peak ʹ BG offers a second means of

quantifying a set of images. The procedure in this case does not involve
images pre-processed using spectral regions or components and therefore
adjustments for time will be included in the calculation. This is neither
appropriate nor desirable for data processed as described in this section, but
is available for use with raw images, where a less sophisticated approach is
adopted.
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RBD Instruments Inc. Auger Scan

PHI Auger instruments upgraded by RBD Instruments Inc export data in ASCII
files or via the clipboard into CasaXPS. The following are a set of case studies
based on data acquired using RBD Auger Scan software.
Auger Scan ASCII files include formats suitable for a single survey spectrum,
the equivalent of a PHI multiplex acquisition consisting of one or more high
resolution spectra or depth profiles relating multiple acquisition cycles to an
experimental variable. The data may be acquired in direct EN(E) mode or as
differentiated spectra.
Survey Spectra
Direct spectra acquired in EN(E) mode provide an opportunity to visualize the
data in the form as acquired:
or numerically differentiated:
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Data acquired in differentiated mode differs in the sense that the baseline to
the data does not necessarily approximate zero.
The original form for these data files:
are essentially the same. Since modern instruments typically acquire the
Auger spectra in direct mode, the data are assumed to be recorded in direct
mode. The implications for the VAMAS file created from these ASCII files are
that the VAMAS fields entered by default may need adjusting for the specific
data type. The most notable information requiring adjustment is the electron
gun energy and the VAMAS technique fields. Both fields influence the ease
with which data are quantified.
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The VAMAS block technique field is assigned by default the value AES dir;
data acquired as differentiated signal should be assigned the technique AES
diff. CasaXPS uses the technique field to determine the type of annotation
information placed over the display when the Region property page on the
Annotation dialog window is applied. For data known to be differentiated,
the Region property page creates a table in which peak-to-peak height
intensity is reported and used to calculate the atomic concentration. If the
data cannot be identified as differentiated, the table offers peak area results.
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An annotation table created from differentiated data either acquired in that

form or externally processed prior to importation into CasaXPS must be
assigned a technique type of AES diff.
Direct data differentiated within CasaXPS automatically displays the

annotation table in terms of peak-to-peak height and peak-to-peak atomic
concentrations. The combination of data assigned the technique AES dir and
the presence of a processing instruction for differentiating the data displayed
via the Processing History property page on the Spectrum Processing dialog
window trigger the display of peak-to-peak annotation table.
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Note: spectra differentiated in CasaXPS, but copied to a new VAMAS block

using the Processed Data Only option will no longer include any processing
history and therefore the technique in the copied VAMAS block should be
assigned a value of AES diff.
Quantification of spectra involves the correct assignment of an RSF to a

transition. RSFs are stored in the element library and to access the
appropriate set of transitions for a particular piece of data also requires the
correct assignment of the electron gun energy in the VAMAS block containing
the data. By default the electron gun energy is assigned a value of 3000 eV.
Many older instruments do not have computer control of the electron gun
and therefore user intervention is required to specify the actual electron gun
energy for the data. The electron gun energy determines the table of RSFs
offered via the element library corresponding to the data displayed in the
active tile. Quantification regions created via the Element Table property
page of the Element Library dialog have RSFs entered into the RSF field based
on the table of library entries visible on the property page. It is therefore
essential that the correct electron gun energy is assigned prior to the
creation of regions.
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A VAMAS block with Source Energy set to 3000 eV and Source Label set to
electron gun results in the Element Table being populated with those library
transitions with Excitation Source string S(3). Similarly, a Source Energy of
5000 eV matches to library entries with Excitation Source string S(5).
Multiplex Auger Spectra

An Auger Scan file may contain more than one spectrum. These spectra
typically represent narrow scan data measured for energy intervals in which
Auger peaks are expected.
When converted to VAMAS format, each of the narrow scan spectra appear
as separate VAMAS blocks.
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Note that these narrow scan spectra, for example, have been exported from
Auger Scan as processed data, where the processing step was that of
numerical differentiation. Data processed externally to CasaXPS are still
converted to VAMAS with technique AES dir and so, to be correct, the
technique field must be manually adjusted to AES diff. For narrow scan data,
the need to set the technique is less important than for survey spectra as
quantification of multiple spectra is typically performed using the Report
Spec page of the Quantification Parameters dialog window where the nature
of the report is specified via configuration files.
In general data exported from Auger Scan may be raw direct spectra, raw
differentiated spectra or processed spectra.
Depth Profile Data

Auger depth profile data are exported from Auger Scan using a distinct
format from data exported as multiplex spectra.
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These data are organised into a VAMAS file using the acquisition region labels
and etch times. The resulting array of VAMAS blocks as viewed through the
right-hand pane of the experiment frame provides the mechanism by which
regions are propagated to data from identical transitions.
A sputter depth profile involves removing material with an ion-gun

interleaved with acquisition cycles where spectra are recorded from each
new surface uncovered by the etching process.
A consequence of etching the material is that the environment for each

surface changes with etch time and therefore the nature of the data alters
too. An interface between layers may cause a change in chemical state for a
transition. For example SiO2 on elemental Si can cause shifts in peak positions
due to charging conditions changing as well as chemical shifts in the peak
positions. Differences in the data over the course of a profile are
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accommodated in CasaXPS by allowing each VAMAS block to maintain region

parameters specific to the spectrum in the VAMAS block.
Regions are created using the Regions property page of the Quantification
parameters dialog window. The regions displayed on the Regions property
page are the regions defined on the VAMAS block displayed in the active tile.
If more than one spectrum is displayed overlaid in the active tile then the
VAMAS block selected first using the right-hand pane is the active VAMAS
block in the active tile. The Regions property page displays the regions
defined on the active VAMAS block in the active tile. Any alterations to region
parameters only apply to the active VAMAS block in the active tile. It is
therefore possible to create regions most appropriate for the individual
spectra by displaying the spectra one at a time in the active tile and making
adjustments appropriate to the spectrum. Typically, such adjustments are
only necessary for a limited number of spectra and the majority of spectra
require essentially the same region parameters. The propagate mechanism
allows a region defined on a spectrum to be propagated to other spectra
based on the selection in the right-hand pane.
For the depth profile under consideration, the oxygen Auger peak is
measured from four different environments.
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Regions for each of these four environments are specified by, in turn,
overlaying the data in the active tile. Creating the first region for the set of
VAMAS blocks displayed in the active tile, followed by propagating the region
to VAMAS blocks containing similar data.
Since propagation of regions is dependent on the selection in the right-hand
pane, options for making selections in the right-hand pane can help target
subsets of VAMAS blocks. The display tiles can be used to collect spectra with
similar requirements, thus aiding the selection and re-selection of VAMAS
blocks in the right-hand pane. The following window illustrates a scenario
where the four environments for the oxygen are displayed in four display
tiles. No VAMAS blocks are currently selected in the right-hand pane.
Each display tile represents a subset of VAMAS blocks. If the Control

keyboard key is held down and the cursor placed over one of the display tiles,
on left clicking the mouse button the VAMAS blocks displayed in the tile over
132
which the cursor resides are toggled into the current selection in the right-
hand pane. Thus, the set of VAMAS blocks displayed in the top right-most
display tile are reselected as follows:
The VAMAS blocks displayed in the tile over which the cursor is placed are
added to the selection such that, if the blocks are already selected, the action
deselects the selected blocks while blocks previously not selected become
selected. Since the propagate operation transfers regions etc to selected
VAMAS blocks, collecting data in display tiles aids the selection and therefore
propagation process. Once the subset of VAMAS blocks has been returned to
the selection in the right-hand pane, adjusting the region parameters for the
block in the active tile naturally leads to the propagation of the changes to
the associated data. Right-clicking the mouse with the cursor over the active
tile invokes the propagation dialog window, thus facilitating the transfer of
changes to all the data displayed in the active tile.
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Once regions have been defined for all the spectra in the profile, a plot of
atomic concentration against etch time is created via the Report Spec
property page.
The Custom Report section on the Report Spec property page offers a means
of tabulating intensities and atomic concentrations as a function of etch time.
These tables in turn are converted to a VAMAS file or exported via the
clipboard to spreadsheet software. The File menu available once the data are
tabulated using the Height button on the Custom Report provides a means of
generated the VAMAS file, while the copy toolbar button places a text form
of the table on the clipboard. These operations are described in earlier
sections of the Auger manual.
The following profile plot is an example of a depth profile created via the File
menu available when the Custom Report results window is the experiment
frame with focus.
134
135
TOF SIMS
The Nature of ToF Spectra
Time-of-Flight Mass Spectrometry (ToF MS) is based on the principle that ions
created from a sample are accelerated into a flight tube using an electric
extraction field resulting in each ion of a given charge acquiring a
characteristic energy from a tight distribution of possible energies. Since the
kinetic energy of the ions are nearly identical, the velocity attained by ions
with differing mass must also differ, thus the time taken for an ion with a
given charge to travel a given distance down the flight tube to the detector
discriminates between ions of different mass. Specifically, the mass of an ion
is proportional to the square of the time taken to travel a fixed distance.
Thus, ToF MS works on the basis of a stop-watch; a start event occurs as the
extraction voltage is pulsed, followed by a sequence of stop events
representing the arrival of ions at the detector. To process a ToF mass
spectrum from the raw timing data, a histogram is created from the set of
time values, where the time events recorded during an experiment are
counted into time-bins. The relationship between the time events and the
mass of the ions responsible for the time events allows the time-bin
histogram to be viewed using a mass scale.
CasaXPS displays the ToF intensities with respect to the time bin indices, even
when a mass calibration is available. Converting a spectrum to mass binned
intensities involves a mapping which cannot be reversed; explicit steps must
be taken to perform the transformation between time and mass.
The following two plots are for the same data, both viewed in the time
domain. The mass range in these two plots is identical.
136
The same spectrum plotted using a linear mass step size changes the
perspective of the data as follows.
Spectra from ToF instruments traditionally appear as a single spectrum over a

wide range of mass. The spectral display reflects the parallel nature of the
technique in the sense that counts are allocated over the entire range of time
bins for each pulse of the ion gun. This is in contrast to quadrupole or
magnetic sector MS instruments where the signal is only recorded one mass
bin at a time. Nevertheless, for high resolution ToF MS the majority of time
bins, particularly at low mass, contain little information, therefore CasaXPS
offers a means of converting ToF spectra from a single monolithic data set
into a set of mass intervals representative of the useful information content.
Each nominal mass, based on the current time to mass calibration, is isolated
into individual VAMAS blocks. Presenting a ToF spectrum as a set of many
137
VAMAS blocks favours the tools within CasaXPS providing the basis for data
comparison and peak analysis via synthetic peak models.
The partitioning of the time bins into suitable mass ranges around the
nominal masses requires a calibration for the mass scale.
ToF Mass Calibration

The relationship between the mass m of an ion and the time taken for the ion
of a given charge to travel a fixed distance is quadratic in the flight time t. For
an ideal system, the time-to-mass relationship is:
m (t 0 ) / b]2
where t0 represents a time offset and b scales the time values appropriately.
Since knowledge of these two parameters t0 and b is sufficient to describe
the relationship between the mass and time-of-flight, given two mass/time
pairs the calibration parameters can be determined from a pair of
simultaneous equations. In reality, assigning the mass/time coordinates from
the time-binned spectra is not exact and therefore the time-to-mass
calibration must be computed in a least-squares sense using multiple
mass/time pairs. Further, the choice of mass/time pairs must be carefully
made to ensure accuracy of the calibration for both interpolated and
extrapolated mass regions. Those mass regions falling within (interpolation)
the set of mass/time pairs used to create the calibration will be more
accurate with respect to the time-to-mass calibration than those outside
(extrapolation) the interval containing the mass/time pairs included in the
138
least squares fit. It is therefore important to calibrate a spectrum using peaks

over as wide a mass range as possible and check that peaks, once calibrated,
can be sequentially assigned to nominal masses. The following describes the
tools in CasaXPS for calibrating a spectrum of time-bins with respect to mass
and how to assess the success of this procedure.
Figure 1
Figure 2: An example of a poor mass calibration based on extrapolation.
When calibrating the mass scale, the primary objective is to assign each
visible peak to a nominal mass. For some spectra and instruments, there may
be perfectly good reasons why this objective may fail, but in general each
peak in the data should be associated with a nominal mass; any mass defect
from the nominal mass provides information about the atomic or molecular
ion responsible for the peak. It is not necessary nor is it always possible to
attribute each peak to a known ion, however, when properly calibrated, if the
observable peaks deviate from the sequence of nominal masses then the
accuracy of the calibration may be in doubt. The problem of calibrating the
mass scale reduces to identifying a set of peaks sufficiently well distributed
over the mass scale to provide plausible mass assignments for each and every
139
peak in the spectrum. Figure 1 is an example of a mass calibration in which

the set of peaks displayed matches well with the computed mass positions;
however the calibration is performed using only those peaks within the
window in Figure 1 and a similar agreement, when using the same
calibration, for the molecules shown in Figure 2 is not achieved. The poor
mass calibration is remedied by simply including at least one of the peaks in
Figure 2 as part of the calibration set. The concept of progressively adding
calibration points to the set used to mass calibrate a spectrum is developed
in following sections.
Calibration Based on Nominal Masses
Figure 3: Nominal mass calibration
The procedure for calibrating a spectrum can be summarised as follows:

following an initial assignment based on at least two peaks, new peaks are
progressively added to the set of mass/time pairs until the observed peaks
are sequentially associated with nominal masses. The spectrum in Figure 3 is
calibrated based on nominal masses and an iterative improvement
procedure. This process can be performed manually using the Exact Mass
property page (Figure 4), where peaks are associated with formulae using the
mouse, or alternatively nominal masses are used in a sequence of steps
involving repeatedly:
1. Finding the peaks using the Find Peaks button.
140
2. Replacing the current calibration list by nominal masses and times

determined from the regions obtained from the Find Peak operation.
The Load Regions button transfers the required information from the
current set of regions to the calibration list on the Exact Mass property
page.
3. Recalibrate the mass scale by pressing the Calib C,t0 button.
Figure 4: Exact Mass Calculator Property Page.
The Find Peaks button uses a threshold to identify peak structures in the
data; then for each peak identified, a region is created on the spectrum using
the name derived from the nominal mass determined from the region. The
Load Regions button transfers those nominal mass names and computed
positions to the calibration table on the Exact Mass property page for which
the computed mass is within a tolerance of the nominal mass. The search for
these acceptable mass/time pairs begins with the low masses, so the initial
calibration should begin with small masses, but typically greater than 10 amu.
With each repetition of these steps, the number of regions loaded into the
calibration table should increase until, ideally, all the peaks found are
included in the calibration table. At this point, the spectrum so calibrated
should be surveyed to ensure the peaks, both minor and major, are
associated with the nominal masses on the abscissa scale.
141
Figure 5: Raw time-binned spectrum.
Calibration using nominal mass values is not always appropriate, for example
heavy molecular ions; however, for some spectra, calibration using exact
masses is equally inappropriate. The data in Figure 1 is an example of a
spectrum for which it is beneficial to use nominal masses rather than exact
masses; the spectrum derives from a total ion list file containing image
information and minor variations in acquisition conditions across the imaged
surface cause small shifts in the underlying peaks summed to form the total
ion spectrum. Peaks are neither high enough in mass resolution nor well
enough defined in terms of position to use an exact mass position. The latter
can be demonstrated using false colour images to extract spectra from
different zones on the image.
An Example of Mass Calibration using Nominal Masses

Initially the spectrum is without a mass calibration as seen in Figure 5. The
first step is to identify two peaks.
Figure 6: Two peaks are identified by creating quantification regions.

142
The regions defined on the spectrum in Figure 6 represent the initial pair of
mass/time coordinates used to produce a rough calibration for the mass
scale. The regions are created using the Regions property page on the
Quantification Parameters dialog window. Each region calculates the time-
bin representative of the peak, while the mass corresponding to the
computed time-bin is entered into the name field of the quantification
region. In this case, the name fields are entered with the nominal masses 15
and 23, although these values could equally well have been entered using the
formulae C+H*3 and Na, respectively. Calibration based on these two regions
is performed by pressing the toolbar button. When the toolbar button is
pressed, any spectra appearing in the Active Tile will be calibrated based on
regions so defined on the displayed spectra.
Figure 7: Spectrum after initial mass calibration.
While the calibration in Figure 7 looks reasonable for masses close to the
calibration points, the high mass peaks are poorly calibrated. The largest
peak in Figure 8 differs by about 18 amu from the mass calibration shown in
Figure 3.
Figure 8: Poor mass calibration for high mass peaks. Same peaks as those displayed using the
inset tile in Figure 3.
143
While the initial mass calibration based to only two low mass peaks is clearly
a problem at higher masses, the accuracy is sufficient to begin the iterative
process of build a fuller set of mass calibration points.
Figure 9: Exact Mass property page.
Figure 10: Result of Find Peaks with a threshold of 20.
Given the initial mass calibration based on the peaks labelled 15 and 23, the
Find Peaks button on the Exact Mass property page shown in Figure 9 can be
used to assign nominal masses to all peaks characterized by a threshold
value. On pressing the Find Peaks button, a dialog window appears in which a
threshold value can be entered. In the case of the results shown in Figure 10
the threshold value was set to 20. Once a new set of regions are created
using the Find Peaks button, the Load Regions button is pressed, the
consequence of which is the mass calibration table on the Exact Mass
property page is loaded with the set of calibration points determined from
the regions currently defined on the spectrum, subject to the condition that
the mass determined from the time bin for each region is within a tolerance
of the nominal mass entered into the name field of the region. Following the
144
initial mass calibration and application of the Find Peaks button, the set of
regions generated by the Find Peaks button in Figure 10 are limited by the
Load Regions button to those displayed in Figure 9. That is, all regions above
nominal mass 31 were sufficiently different from the nominal mass to be
rejected. The deviation of the computed mass for peaks above 31 amu from
the nominal mass is a measure of the error in the original mass calibration.
Given the new set of calibration points, the Calib button on the Exact Mass
property page can be pressed resulting in an improved mass calibration.
Repeating the Find Peaks operation followed by reloading the regions into
the calibration table reveals that peaks up to 53 amu are now included in the
calibration table. A third iteration of these steps produced a calibration table
including peaks up to 228 amu, while a forth iteration extends the calibration
table up to 561 amu, exhausting the set of peaks found using the Find Peaks
button. The mass calibration based on nominal masses is now complete. All
that remains is to verify the mass calibration by stepping through the spectral
peaks to confirm the presence of peaks at each amu and that known peaks
are correctly assigned.
Figure 11: High resolution ToF peaks clearly distinct from the nominal mass of 28 amu.
The procedure is not without flaw, so verification is necessary, but can

provide a means of improving an initial calibration with minimal effort. For
high resolution ToF spectra, the use of nominal masses will lead to a rough
mass scale which requires refinement using resolved peaks and exact mass
formulae (Figure 11).
NB: The peak marker in Figure 11 for elemental Si is positioned to the left-
hand side of the peak. When a ToF spectrum is calibrated using the option on
the toolbar, the position of peaks with respect to time are determined from
the regions. While the peak maximum may appear to be a good choice for
145
the peak position, the asymmetry typically observed in ToF peaks and the
variety of peak shapes over a spectrum suggest, in general, the peak
maximum is less well defined than the leading edge of a peak. For this
reason, the position of the peak used for the calibration procedure is taken to
be the lower full width half maximum. Hence the peak markers will align with
the leading edge of the peaks rather than the peak maxima. Note that the
calibration option on the Exact Mass property page offers the choice of peak
position to the user without limitation.
Recalibration of Mass Scale for ToF Spectra

Occasionally ToF Spectra are supplied as mass binned data. While data in
mass bins is convenient for those without the ability to handle the relatively
large time binned spectra, the possibility exists that the mass calibration used
to mass-bin the spectra may not be accurate enough for the application in
question. For high resolution mass spectra, a small error in the original time-
to-mass calibration may lead to the type of uncertainty illustrated in Figure
12, where the peak maximum falls between the two most likely assignments
for the measured data. A recalibration of the mass bins is therefore required.
Figure 12: An example of a mass-binned spectrum where the original mass calibration is not
sufficiently accurate for the resolution of the peak shown.
The recalibration of mass-binned data differs from a time-to-mass calibration

of time-binned data in that the act of reallocating the counts to mass-bins
from the original time-binned data (performed during the creation of the
mass spectrum), results in the loss of information. Namely, two or more
time-bins may map into the same mass-bin, therefore it is impossible to take
a mass-bin and repopulate the time-bins with the same distribution found in
the original data set. The consequence of there being a fundamental
146
difference between these two operations is that, when recalibrating a mass-

binned spectrum, the functional form used to assign the data bins to mass
values must involve a general three parameter quadratic function rather than
the stiffer model used to calibrate time-bins to mass-bins. The two parameter
calibration function recommended for time-to-mass calibration is too specific
to the counting mechanism used to acquire the ToF MS data. The extra
flexibility offered by the three parameter quadratic is needed to model the
errors in the original time-to-mass calibration; the stiffer two-parameter
quadratic model used for time-to-mass calibration is dictated by and
appropriate to the physics of the ToF instrument.
While CasaXPS allows time-to-mass calibration using both the recommended
two-parameter quadratic model and the general three-parameter quadratic
function, the same warning about the three-parameter functional form is
equally applicable to both situations. That is, the flexibility offered by the
general quadratic function allows non-physical solutions for the mass
assignment of peaks. It is possible to create a mass calibration when using
the three-parameter quadratic for which known peaks are apparently
correctly assigned to masses, yet other peaks in the spectrum are incorrectly
assigned. Extrapolation based on the three parameter model should be
viewed with suspicion. Ideally, ToF MS data should be provided in the time
domain, nevertheless situations do occur where mass-binned data must be
managed and therefore CasaXPS provides a mean of recalibrating the mass-
binned data. Figure 13 shows the same data seen in Figure 12 following the
recalibration procedure described below.
Figure 13: The same mass spectrum after recalibration.
147
Recalibration Steps
1. Cancel the Mass calibrated status of the spectra: overlay the mass-
binned spectra in the Active Tile and press the toolbar button on
the SIMS toolbar. The label ĨŽƌƚŚĞĂďƐĐŝƐƐĂǁŝůůƌĞƚƵƌŶƚŽ͞dŝŵĞŝŶ͕͟
which indicates the data is in a state where a new calibration can be
created. Note, the abscissa values will be bin indices, not true time-
bins, but nevertheless it is necessary to the calibration procedure that
ƚŚĞĂďƐĐŝƐƐĂůĂďĞůŝƐĂƐƐŝŐŶĞĚƚŚĞƐƚƌŝŶŐ͞dŝŵĞŝŶ͘͟
2. Using the Exact Mass Calculator, a new calibration set defining the
relationship between the peaks and the mass assignment must be
established. The procedure is identical to creating a time-to-mass
calibration described elsewhere.
3. Perform the recalibration using the button on the Exact Mass
Calculator property page of the Element Library dialog window.
Figure 14: A mass-binned peak illustrating the peak deformations due to the re-binning
algorithm used to create the mass spectrum.
An alternative procedure is to create quantification regions and apply the

recalibration using the toolbar button. While possible, this approach
suffers from the information lost during the time-to-mass conversion
procedure, that is, the mass-bins for higher mass values tend to be poorly
defined compared to the original time data (Figure 14). The algorithms for
identifying a peak position and therefore determining the calibration points
148
assumes the data obeys Passion statistics, but otherwise varies smoothly; it is
clear from Figure 14 that the mass-binned data contains anomalous values.
Peak Fitting ToF SIMS Data

The features in CasaXPS typically used to model XPS data envelopes can also
be used to analyst overlapping peaks in high resolution ToF SIMS spectra. The
principal difference between ToF SIMS and XPS is that asymmetry in ToF
SIMS peaks is, in general, in the opposite direction to that found for XPS
peaks. As a result, not all line-shapes in CasaXPS are appropriate for ToF SIMS
peaks, however the more recently introduced asymmetric line-shapes of LA
and LF provide a means of creating line-shapes appropriate for the range of
ToF SIMS peaks observed in practice.
The data in Figure 15 illustrates the similarities between XPS and ToF SIMS,
where the mass peaks associates with a nominal mass of 42 are very typical
of polymer XPS spectra such as PMMA or PET. The problems of
understanding the data are also similar in that both the position and the
intensity of the underlying peaks are of importance when identifying the
molecular ions responsible for the measured data.
Figure 15: Example of ToF SIMS peak structure.
The procedure for adding synthetic components to the data involves first
adding a quantification region to the data witŚďĂĐŬŐƌŽƵŶĚƚǇƉĞƐĞƚŽĨ͞ĞƌŽ͟
before adding synthetic line-shapes. Creating and adjusting regions and
components is performed on the Quantification Parameters dialog window
149
available from the Quantify option on the Options menu or the toolbar
button on the top toolbar of CasaXPS. Regions and components are managed
using the tables found on the Regions and Components property pages of
the Quantification Parameters dialog window shown in Figure 16.
The peaks shown in Figure 15 are defined using the parameters displayed in
the table on the Components property page illustrated in Figure 16. The line-
shape parameter in this example is defined using the LA functional form,
where the parameters provide a degree of asymmetry to the right of the
peak maximum. The meaning of these parameters is described below.
Figure 16: Quantification Dialog Window.
Line-shapes Suitable for ToF SIMS Spectra

The success of a peak fit is dependent on an appropriate choice for the line-
shape parameter. As stated above, the LA and LF line-shapes offer sufficient
flexibility for most ToF SIMS peak shapes.
The Lorentzian line-shape with FWHM F and position M is given by
1
L ( x : f , e) 2
(1)
x e
1 4
f
The functional form is symmetrical about x = M. In order to retain the
characteristics of the Lorentzian line-shape and yet also introduce
asymmetry, the LA line-shape is defined in two halves as
150
(2)
>;ɲ͕ɴ͕m): Equation (2) defines the first two parameters used in the line-
shape >;ɲ͕ɴ͕m) shown in Figure 16. The third parameter m is used to
control the width of a Gaussian convolution applied to the functional form
defined by Equation (2). As a consequence of the definition for the LA line-
shape, an asymmetry line-shape is established by specifying ɲ not equal to ɴ.
Further, is ɲ is greater than ɴ then the resulting peak will be asymmetric with
an extended tail to the right of the peak maximum. Adjusting the Gaussian
convolution parameter causes the extent of the asymmetric tail to reduce
and also shifts the peak maximum towards the extended tail.
>&;ɲ͕ ɴ͕ w, m): Identical to the LA line-shape with the exception that the
specified values of ɲ and ɴ are force to increase to a constant value via a
smooth function determined by the width parameter w. The w parameter is
used to restrict the extent of the tail.
Figure 17: Asymmetric Mass Peak fitted using a single LA line-shape.
By way of example, the elemental sodium mass peak shown in Figure 17

exhibits significant asymmetry to the right of the peak maximum, which can
be modelled using the LA line-shape. Note that the line-shape included in the
annotation of the peak in Figure 17 is achieved by setting the first parameter
to a value greater than unity, thus compressing the tail to the left compared
151
to the tail to the right. Further, the Lorentzian tail to the right of the peak
maximum is adjusted by convoluting the functional shape with a Gaussian of
characteristic width described by a value of 250 for the m parameter in the
LA definition. The degree of asymmetry is determine by the relative size of
the first parameter compared to the second, that is ɲ > ɴ.
Figure 18
The line-shape used in Figure 17 should be compared with the line-shape in

Figure 18 corresponding to a similar sodium peak measured using the same
IonToF instrument but using a different ion gun. The peak in Figure 18 rises
more quickly than ƚŚĞ ƉĞĂŬ ŝŶ &ŝŐƵƌĞ ϭϳ͕ ƚŚĞƌĞĨŽƌĞ ƚŚĞ ɲ-parameter is now
much larger than ƚŚĞɴ-parameter, which is also set to a value greater than
unity. The larger the values for these two parameters the steeper the edge of
the peak appears. Also note in Figure 18 that the Gaussian convolution is
much narrower than that used in Figure 17. Possible values for the Gaussian
parameter are between 0 and 499; m = 0 corresponds to no convolution
being performed.
Peak Identification and Reduction

High resolution ToF spectra typically consist of numerous peaks, however for
some analyses only a small number of correlated peaks are significant for
152
distinguishing between samples. That is, a peak at one mass is only

characteristic of a particular compound when also accompanied by peaks at a
set of very specific masses. Given the plethora of peaks typically present in
ToF MS data, a means of grouping and displaying only significant peaks is
required. To visualise the spectrum with respect to only significant peaks, a
ToF spectrum can be organised in CasaXPS 2.3.15 such that the Element
Library property page simplifies the mechanism by which these significant
peaks can be displayed for visual inspection. In addition to the element
marks, a spectrum can be broken into an array of VAMAS blocks representing
the peak information associated with the nominal masses and the element
library used to display appropriate subsets of these VAMAS blocks for
interpretation.
The procedure for splitting a ToF spectrum into a set of mass calibrated
VAMAS blocks can be performed using the toolbar button indicated in Figure
19. As an alternative approach, for data files for which a mass calibration is
available to CasaXPS at the time of conversion the division of the data into
mass calibrated VAMAS blocks can be performed at the time the data are
converted. Either route to the mass calibrated VAMAS blocks requires a mass
calibration for the data.
Figure 19: ToF Spectrum with data in time domain.
153
The data in Figure 19 are converted to a mass calibrated set of VAMAS blocks
by pressing the toolbar button with hint Split into Unit Mass Spectra. The
result of converting the data in Figure 19 is shown in Figure 20, where the
right-hand pane displays the set of VAMAS blocks derived from the single
VAMAS block in Figure 19.
The display in Figure 20 is achieved by overlaying the full set of VAMAS blocks
from the right-hand pane in the active tile. An inset tile is used to display a
specific VAMAS block, namely the VAMAS block corresponding to a nominal
mass of 42. Note that since the individual VAMAS blocks are mass calibrated,
the overlay appears in the form of a mass calibrated spectrum.
Figure 20: ToF Spectrum after conversion to mass calibrated VAMAS blocks.
The discussion that follows relates to data prepared in the format shown in
Figure 20. Presenting the spectrum as a set of VAMAS block provides the
basis for the tools within CasaXPS. Before describing these tools, the method
for converting data files directly to mass calibrated sets of VAMAS blocks will
be addressed. Version 2.3.15 of CasaXPS only offers data conversion to the
multiple VAMAS block format for ASCII files formatted using the convention
adopted by the IonToF data system.
IonToF Peak Identification

IonToF spectra are exported in ASCII files in the format shown in Figure 21.
The follow describes the options in CasaXPS for importing these data in
formats suitable for compiling peak lists.
154
Figure 21:IonToF ASCII format.
The SIMS toolbar in CasaXPS offers two toolbar buttons for controlling the
import of data in the format shown in Figure 21. These toolbar buttons are
indicated in Figure 22.
Figure 22: SIMS Toolbar buttons
The traditional method for working with ToF data is based on a single data
block approach, however the tools for peak identification now added to
CasaXPS are organized on a partitioning of the data into numerous data
blocks based on the nominal mass for each group of peaks. The objective is to
analyze a directory of spectra and determine a set of mass peaks and
intensities for each spectrum in the directory.
Converting IonToF Spectra
Figure 23: ASCII txt files exported from the IonToF software.
155
A data directory initially contains a set of spectra exported from the IonToF
software as ASCII txt files. Figure 23 illustrates such a directory which is
displayed using the File Dialog window offered by the toolbar button. The
conversion of these data may be performed using several filter strings as
follows:
1. ͘͞ŝŽŶ͟
2. ͘͞ĂŵƵ͟
3. ͘͞ƐƵŵ͘͟
To initiate a conversion sequence, a name followed by one of the above
strings must be entered into the File name text-field on the File Dialog in
Figure 23. For example, to convert and merge the set of txt files in a format
suitable for peak identification, the File name text-field should be entered
ǁŝƚŚ ƚŚĞ ƐƚƌŝŶŐ ͞ĚĂƚĂĨŝůĞ͘ĂŵƵ͘͟ dŚĞ ďĂƐĞ-name is arbitrary, however the
ĞǆƚĞŶƐŝŽŶ ͘͞ĂŵƵ͟ ŝŶƐƚƌƵĐƚƐ the set of txt files to be converted to VAMAS
format (a new VAMAS file will appear in the directory for each txt file
processed) then these converted files are merged into a single experiment
frame in CasaXPS. Note that these data are large; therefore the process is
both time consuming and requires plenty of PC memory!
The different filter strings determine the nature of the data files generated
from the IonToF ASCII files. The individual VAMAS files generated from the
ASCII files are identical for both thĞ ͘͞ĂŵƵ͟ ĂŶĚ ͘͞ƐƵŵ͟ ĨŝůƚĞƌƐ͖ ƚŚĞ ĨŝŶĂů
ŽƵƚĐŽŵĞĚŝĨĨĞƌƐŚŽǁĞǀĞƌ͕ǁŚĞƌĞƚŚĞ͘͞ĂŵƵ͟ĨŝůƚĞƌĐĂƵƐĞƐƚŚĞŵĞƌŐĞƌŽĨƚŚĞ
spectra into a single experiment frame as separate spectra equivalent to the
ŽƌŝŐŝŶĂů^//ĚĂƚĂ͕ǁŚŝůĞƚŚĞ͘͞ƐƵŵ͟ĨŝůƚĞƌƌĞƐƵůƚƐŝŶƚŚĞƚŽƚĂůcounts from the
set of spectra in the ASCII files forming the equivalent of a single mass
spectrum. In both cases, the mass spectrum from each of the IonToF files is
partitioned into VAMAS blocks corresponding to data in the vicinity of the
nominal mass vaůƵĞƐ͘&ŝŐƵƌĞϮϰƐŚŽǁƐƚŚĞƌĞƐƵůƚŽĨƵƐŝŶŐƚŚĞ͘͞ƐƵŵ͟ĨŝůƚĞƌŽŶ
the data directory depicted in Figure 23. Both display tiles in Figure 24 display
an overlay of all the data blocks in the right-hand pane of the experiment
frame and the inset tile shows the data from the three highlight blocks
containing intensities for nominal masses 41, 42 and 43 amu.
156
Figure 24: Example of a total counts spectrum formed from the four ASCII files shown in
Figure 23.
dŚĞĐŽŶǀĞƌƐŝŽŶĨŝůƚĞƌ͘͞ŝŽŶ͟ǁŚĞŶ applied to a directory merges the data into

a single experiment frame containing one spectrum per original ASCII file, but
maintains the data for each spectrum as a single block. While the format
adopted is more traditional for mass spectra, the peak identification option
uses peak-fitting and therefore the format shown in Figure 24 is more suited
ƚŽƚŚĞĂůŐŽƌŝƚŚŵƐŝŶǀŽůǀĞĚ͘dŚĞƐŝŶŐůĞďůŽĐŬŽĨĚĂƚĂƉƌŽǀŝĚĞĚďǇƚŚĞ͘͞ŝŽŶ͟ŝƐ
for visual inspection of the full data set and should not be used when peak
identification is employed.
Directory Profiling
The objective addressed by the features described here, is to identify and
quantify in terms of mass assignments and intensities the set of peaks
characteristic of a sample. The peak structures within a ToF spectrum are
illustrated in Figure 25, where it can be seen that at least five overlapping
peaks to varying degrees are responsible for the data envelope. Peak
intensity and peak position are determined for these types of peak structures
using optimized peak modelling. The very fact that peak modelling is required
highlights the difficulty of automatically identifying all the peaks for a given
data envelope. For a directory of similar spectra, automatically identifying
mass peaks from data such as that in Figure 25 is fraught with dangers and
therefore the strategy in CasaXPS for processing directories of similar spectra
is one of aiding the construction of a template spectrum, for which peak
models are prepared to be exhaustive with respect to the data under
analysis, then the automatic application of the template models to a
157
directory of spectra forms the basis for extracting the quantitative

information for each spectrum in the directory.
Figure 25: Mass peak structure from a ToF spectrum.
The creation of peak models for each significant mass peak in a file such as
the one shown in Figure 24 is central to the profiling options in CasaXPS.
About 500 data blocks corresponding to the nominal masses potentially
require the construction of regions and synthetic peaks. The success of the
template approach relies on the peak models adequately describing the
peaks with appropriate constraints in terms of relative positions and FWHM
to permit the peak intensities to be calculated from the fitted model. To
assist this initial step, an option on the Exact Mass Calculator property page
of the Element Library dialog window offers a means of creating peak models
based on a threshold limit.
The Create Peaks button on the Exact Mass Calculator property page (Figure
26) uses the threshold value to limit the number of peaks created for a given
data block.
Figure 26: Exact Mass Calculator Property page.

158
The peak creation mechanism uses the threshold value entered on the MS
Peak Threshold dialog window to create a region and synthetic peaks for
each data block overlaid in the active tile. The smaller the threshold values,
the smaller the peaks will be that are included in the peak search. Since the
significance of mass peaks may not depend entirely on peak intensity, it is
worth noting that different threshold values may be appropriate for different
ranges in the mass scale. It is therefore unlikely that a single application of
the Create Peaks button will generate all the appropriate peaks, however, by
the user selectively overlaying data blocks and choosing different thresholds,
peaks can be created on large numbers of data blocks while still retaining the
discretion of the operator. Ultimately, the success or failure of the profiling
step will depend on the way these peak models are constructed and time
spent in getting these models right will be recovered by the accuracy and
automatic application of these models to larger data directories.
Profile Directory Toolbar Option

The options for profiling a directory of IonToF spectra are as follows:
1. ͘͞ĂŵƵ͟
2. ͘͞Ĩŝƚ͟
3. ͘͞ǀĨĐ͟
These conversion filters are used to control the nature of the directory
profile. On providing a base name followed by one of these filter strings, the
directory located by the File Dialog window invoked by the toolbar button
is scanned for the appropriate file types and, on accepting the Continue
prompt via the resulting message dialog, the set of files are one-by-one
processed to produce several text file reports and a VAMAS file containing
the profile information from the directory.
dŚĞƚǁŽƉƌŽĨŝůĞĨŝůƚĞƌƐ͘͞ĂŵƵ͟ĂŶĚ͘͞Ĩŝƚ͟ďŽƚŚƌĞƋƵŝƌĞĂƚĞŵƉůĂƚĞƐƉĞĐƚƌƵŵƚŽ
be loaded and displayed in tŚĞ ĂĐƚŝǀĞ ƚŝůĞ͘ /Ŷ ƚŚĞ ĐĂƐĞ ŽĨ ƚŚĞ͘͞ĂŵƵ͟ ƉƌŽĨŝůĞ
filter, the ASCII .txt IonToF files are converted to VAMAS files before applying
the template information to these newly converted data, which are also
saved in the processed state as .vms files. On completion, several text files
provide the results of the profile, one offering the context information for the
numerical tabulations located in the other files. In addition, the profile
information is presented in VAMAS format within the current CasaXPS
session.
159
dŚĞ ƐĞĐŽŶĚ ƉƌŽĨŝůĞ ĨŝůƚĞƌ ͘͞Ĩŝƚ͟ ƉĞƌĨŽƌŵƐ ƚŚĞ ƐĂŵĞ ƐĞƋƵĞŶĐĞ ŽĨ ƐƚĞƉƐ ĂƐ ƚŚĞ
͘͞ĂŵƵ͟ǁŝƚŚƚŚĞĞǆĐĞƉƚŝŽŶƚŚĂƚƚŚĞĨŝůĞƐƉƌŽĐĞƐƐĞĚĨƌŽŵƚŚĞĚŝƌĞĐƚŽƌǇĂƌĞƚŚĞ
͘͞ǀŵƐ͟ ĨŝůĞƐ͘ dŚŝƐ ƌĞŵŽǀĞƐ ƚŚĞ ĐŽŶǀĞƌƐŝŽŶ ƐƚĞƉ ĨƌŽŵ ƚŚĞ ŽƉĞƌĂƚŝŽŶ ĂŶĚ ŝƐ
appropriate if, for example, the data directory has been previously processed
ƵƐŝŶŐ ƚŚĞ ͘͞ƐƵŵ͟ ĐŽŶǀĞƌƐŝŽŶ ĨŝůƚĞƌ ĚĞƐĐƌŝďĞĚ ĂďŽǀĞ͘ dŚĞ ͘͞ƐƵŵ͟ ĐŽŶǀĞƌƐŝŽŶ
filter generates a single spectrum from a set of files in a directory and also, as
part of the process, converts the ASCII files to VAMAS format. The total
ĐŽƵŶƚƐƐƉĞĐƚƌƵŵĐƌĞĂƚĞĚĨƌŽŵƚŚĞ͘͞ƐƵŵ͟ŽƉĞƌĂƚŝŽŶŵĂǇĂƉƉĞĂƌŝŶƚŚĞƐĂŵĞ
ĚŝƌĞĐƚŽƌǇĂƐƚŚĞĐŽŶǀĞƌƚĞĚĨŝůĞƐ͕ďƵƚƉƌŽǀŝĚĞĚƚŚĞĨŝůĞŶĂŵĞƌĞƚĂŝŶƐƚŚĞ͘͞ƐƵŵ͟
sub-string, the total spectrum will not appear in the final profile results
generated from applying the template file to the set of .vms files in the
current directory.
Ŷ ĂůƚĞƌŶĂƚŝǀĞ ǁĂǇ ƚŽ ƉƌŽĨŝůĞ Ă ĚŝƌĞĐƚŽƌǇ ŽĨ ͘ǀŵƐ ĨŝůĞƐ ŝƐ ƚŽ ĂƉƉůǇ ƚŚĞ ͘͞ǀĨĐ͟
profile filter. In this case, no fitting is performed, but rather the existing peak
fits within the set of VAMAS files is used to construct the profile information.
dŚĞ ͘͞ǀĨĐ͟ ƉƌŽĨŝůĞ ĨŝůƚĞƌ ĂůůŽǁƐ ƚŚĞ ŝŶĚŝǀŝĚƵĂů ĨŝůĞƐ ƚŽ ďĞ ŝŶƐƉĞĐƚĞĚ ĂŶĚ ĂŶǇ
anomalies rectified on a file-by-file basis before creating the profile
information. It is important that the same set of VAMAS blocks and number
of synthetic peaks are used on each of the data blocks, however profiling the
directory without automatic peak fitting allows user-intervention to override
poor fitting scenarios.
Working with ToF Spectra in CasaXPS

Time to Mass Calibration Procedures
A raw ToF spectrum is recorded in the time domain. Mass calibration of a ToF
spectrum is performed in CasaXPS by identifying a set of peaks in the data
with specific masses; then, by using these pairs of mass/time values a
quadratic relationship between the time and mass scales is created. A linear
least squares procedure determines the two constants within the quadratic
expression and therefore two or more mass/time pairs must be supplied to
perform the calibration procedure. The accuracy of the mass-to-time
calibration is dependent of the precision of the mass/time pairs used in the
least squares calculation; the more pairs used to compute the least squares
solution, the more tolerant the calibration will be to errors in the mass/time
specification.
160
CasaXPS offers two methods for calibrating ToF MS data:

1. Peaks and corresponding masses specified using quantification regions.
2. Mouse identification of the peaks coupled with an exact mass
calculator located on the Element Library dialog window.
Mass Calibration using Regions and Propagation of Regions

between Spectra
The Quantification Parameters Dialog window provides a means of
defining time intervals, within which systematic positions are defined
(computed from a peak bounded by an interval) and linked to masses via an
exact mass formula entered into the Name field for the regions.
Figure 27: Quantification Parameters Dialog Window shown three regions defined for the
purpose of calibrating the time scale to mass.
The spectrum in Figure 27 is an example of ToF SIMS data where three

quantification regions are defined suitable for calibrating the time scale to
mass. The mass associated with each region is entered into the Name field
and may be a numerical value exemplified by the region headed column B or
a string corresponding to any exact mass formula equivalent to expressions
use on the Exact Mass property page of the Element Library dialog window.
161
For example, the mass of a peak might be defined using the expression
C+H*3, which when evaluated would result in a mass of 15.0235 Daltons.
Mass Calibration
One or more time domain spectra can be prepared with calibration regions as
described above and overlaid in the active tile in the left-hand pane of the
experiment frame. On pressing the toolbar button, each spectrum in the
active tile is calibrated using the peaks within the regions. Since multiple
spectra can be mass calibrated using a single invocation of the toolbar
button, the use of this procedure is supported by the propagation of the
calibration regions to similar spectra, thus avoiding the need to manually
create regions for each spectrum requiring a mass calibration.
Propagation of Calibration Regions

The procedure to propagate the calibration regions from the spectrum as
defined in Figure 27 to two other similar spectra is as follows:
1. Select the VAMAS blocks in each of the two experiment frames
containing the spectra requiring the calibration regions.
The CasaXPS window is arranged in a tiled format using the Tile option from
the Window menu at the top of the CasaXPS main window. The arrangement
of the experiment frames allows the selection to be made by left-clicking the
first VAMAS block in the experiment frame to the bottom-left and then
holding the Control-Key down and left-clicking the VAMAS block in the
bottom-right experiment frame
162
2. The Browser Operations dialog window is invoked by right-clicking the

mouse with the cursor over the left-hand pane of the top-most
experiment frame. The objective is to right-click over the display tile in
which the spectrum containing the calibration regions is displayed.
3. To propagate regions to the two selected VAMAS blocks, which are

listed on the Browser Operations dialog window, tick the radio button
in the Propagate section of the dialog window and press the OK
button. Region labels are now visible on the spectra.
The data in each of the three experiment frames are calibrated by switching
focus between the experiment frames and each time pressing the toolbar
163
button. Control-TAB moves the focus between the experiment frames within
CasaXPS.
The time to mass calibration for the time domain data may be seen labelling
the x-axis using a quadratic mass scale.
Mass Calibration using the Exact Mass Calculator Property Page:

The procedure for calibrating a spectrum involves creating a set of
mass/time-bin pairs within the scrolled-list on the Exact Mass property page
on the Element Library dialog window.
The example below illustrates how the columns in the scrolled-list headed
Mass and Time store the information relating these two parameters. Before
an assignment for a given entry has been made, the value in the Time column
is set to -1. The mass for an entry in the table is computed from the chemical
formula entered into the name column.
164
To add an entry to the calibration table:

1. Type a chemical formula into the text-field below the scrolled list and
press the Add Formula button or press the return key on the keyboard.
The formula for an ion may be entered using the chemical symbols
used to on the Periodic Table property page of the Element Library
dialog window.
2. Select the name in the scrolled-list. To select a name field, place the
cursor over the text within the Name column and left-click the mouse.
The name entry will appear highlighted when successfully selected.
3. Zoom into the known peak in the spectrum displayed in the active tile.
It is important to perform the zoom operation before step 4 is taken.
4. Tick the tick-ďŽǆůĂďĞůůĞĚ͞ĞĨŝŶĞdŝŵĞ͘͟
5. Using the mouse cursor, click on the known peak at a location
representative of the mass already defined by the selected entry in the
scrolled list. The value in the Time column is updated and the Define
Time tick-box is cleared.
At least two entries must be specified in the scrolled-list before pressing the
Calib C,t0 button on the Exact Mass property page. The more entries
assigned mass/time pairs, the better the mass to time calibration will be
computed in the least squares sense.
Once a calibration table has been prepared, a file containing the calibration
points can be saved to a separate text file from the data.
165
These files can be reloaded at a later time to provide an initial calibration for
other data or for making adjustments to the calibration of the original
spectrum used to create the calibration file. Note, while the Save button on
the Exact Mass property page saves the current calibration table, the Load
button will merge a saved file with the current set of entries on the scrolled-
list. To return the table to the entries within a file, it is first necessary to press
the Delete All button. The Delete All button removes the current entries in
the scrolled-list, while the Delete Entry button removes the currently
selected entry.
If an assignment is incorrect, the individual entry must be deleted from the
table. The name field for the deleted entry is entered into the text field
below the scrolled list; therefore a selected entry can be deleted then
reinstated by immediately pressing the Add Formula button. The Time field
will return to a value of -1 and therefore be ignored during any subsequent
calibration operation.
The Element Library from a ToF Perspective

The element library in CasaXPS is an ASCII file. On startup, CasaXPS loads the
default element library from within the same directory as the one in which
the CasaXPS.exe executable file is located. The name of the default element
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library file is CasaXPS.lib and is designed with the view that the element
library can be constructed for specific applications. For example, in the case
of quadrupole MS, a library consisting of elemental isotopes is appropriate to
the resolution of quadrupole mass spectra, while for high resolution ToF MS
a library consisting of entries for molecular fragments is required when
assigning mass peaks.
Preparing an element library file for mass spectra may be performed using a
spreadsheet program such as Excel or tools on the Exact Mass Calculator
property page allowing correctly formatted library files to be constructed
from lists of chemical formulae. Methods for displaying the significant peaks
based on selections from an element library constructed from one or more
library files are described below.
The Element Library and Linking ToF Peaks for Display

High resolution ToF spectra typically consist of numerous peaks; however for
some analyses only a small number of correlated peaks are significant for
distinguishing between samples; a peak at one mass is only characteristic of a
particular compound when also accompanied by other peaks in the
spectrum. A strong link between the element library and displaying data for
inspection is therefore introduced in CasaXPS 2.3.15. The objective is to use
the element library to specify a set of mass peaks grouped with respect to
correlated peaks which are used to makes selections of VAMAS blocks. These
selections of VAMAS blocks containing narrow interval mass spectra combine
with the display tools in CasaXPS to provide a perspective in which overall
spectral distribution and localised peak structure can be assessed with
relative ease.
A ToF data set presented as a set of unit mass VAMAS blocks can be viewed
in the more traditional form of a single plot. The traditional perspective of a
ToF spectrum is achieve by selecting all the VAMAS blocks in the right-hand
pane, then pressing the overlay toolbar button. When viewed as a single
continuous display, all the features for manipulating the display are still open
for use.
167
The advantage of creating a set of mass calibrated VAMAS files is that the
spectrum can be dissected and displayed with a variety of options:
Display only those peaks more than 5% in intensity of the largest peak.
Display one VAMAS block per tile for those peaks greater than 5% of the
maximum peak. All peaks scaled with respect to a specific peak; mass 23 in
this case.
168
Scale the peaks on an individual basis.
Take a closer look at specific peaks.
Enhancements for manipulating the selection and display for ToF MS data are
available on the Element Table property page of the Element Library dialog
window.
169
The mechanisms offered on the Element Table property page are described
in the following sections.
Linking Element Library Entries

A CasaXPS library file may be prepared with a set of entries corresponding to
particular sample chemistry. Such a library file can be loaded or merged with
the existing library file whenever appropriate. The essential feature of the
entries in the given library file is that a set of mass formulae are all assigned
the same unique string for the Transition column.
Using the Selection Mechanism

By way of example, a set of formulae only involving carbon and hydrogen are
assigned the Transition string CH. On selecting one of the entries using the
Name column of the table on the Element Table property page bearing the
CH Transition string before pressing the Display Linked VBs button on the
Element Table property page causes all those VAMAS blocks (in the
experiment frame with focus) to be displayed in the left-hand pane, one
VAMAS block per tile. Thus, a set of related mass peaks can be easily
displayed for inspection.
170
A dialog window provides a means of only selecting those VAMAS blocks for
which the peak intensity is greater than the specified percentage of the
maximum peak in the data.
The key used to match the VAMAS blocks in the experiment frame is the
string corresponding to the Species VAMAS field within each VAMAS block.
The Species VAMAS field is used in the header string for each column of
blocks in the right-hand pane of the experiment frame.
The ToF spectral files, when split into sets of VAMAS blocks, are created using
the appropriate nominal masses to create these Species fields and the library
entries with the common Transition library field are used to compute the
corresponding nominal mass for each library entry, which when matched to
the Species VAMAS fields causes the data to be displayed in the tile list.
171
The element library file also includes Transition strings CO and F.
The different assignments for the Transition strings are simply a partition of
the file between three possible sets of mass peaks; however a more realistic
example might involve significant peaks from any combination of mass peaks,
all of which would be collectively assigned a common Transition string.
Should the same mass peak correspond to more than one compound, the
element library file can include repeated entries differing only by the
Transition string.
Overlaying Related VAMAS Blocks

The Element Table property page also includes a button for overlaying
VAMAS blocks selected from the current file using the same mechanism as
the Display Linked VBs button described above.
172
To overlay a set of VAMAS blocks corresponding to a predefined compound,

one of the entries in the element-table list for the compound is selected
before pressing the Overlay Linked VBs button. A dialog window appears
offering a threshold value, which represents the percentage of the maximum
height intensity of the peaks in the experiment frame. Only peaks of intensity
greater than the percentage specified on the dialog window will be included
in the set of VAMAS blocks overlaid in the active tile.
Constructing an Element Library File

The element library file was constructed using the Ex M T button on the Exact
Mass property page and three text files containing lists of chemical formulae.
An example file containing formulae used to compute exact masses for
library entries is as follows.
To create a corresponding library file, select the text file via the File Dialog
invoked by the Ex M T button.
The base-name for the text file is used to assign a string to the Transition field
in the resulting library file created when the Open button is pressed on the
File Dialog window. The new library file appears in the directory where the
original text file is located.
173
The intension is that a text file is prepared for those mass fragments
characteristic of a particular compound, from which a library file is then
created. When it is desired to visually inspect a ToF spectrum for evidence of
the given compound, the library file for the compound is loaded into CasaXPS
via the Input File property page.
The library file displayed via the Element Table scrolled list
174
is a combination of loading three different library files using the Input File
property sheet. The first file was selected using the Browse button, and then
pressing the Load button caused the selected library file to replace the
existing library entries. The two remaining files were merged with the first
file by again using the Browse button to select the files followed by pressing
the Merge button.
Examining the Peak Structure using Zoom Actions

The standard method for defining a range of intensities in CasaXPS is to use
the left-mouse button to drag a box over the peaks of interest before left-
clicking inside the box on the display tile. The mechanism used in the
definition of the zoom-box is enhanced when the Element Table property
page is top-most on the Element Library dialog window. These enhancements
are enabled by holding down the Control Key or the Control Key at the same
time as the Shift Key on the key board. The result of combining the Control
Key with the Element Table top-most on the Element Library dialog window is
to create a narrow and tall zoom box at the location of the cursor whenever
the left-mouse button is clicked.
The second modification to the zoom mechanism is designed to provide a

means of creating a limited intensity applicable to the mass range currently in
effect. Holding down the Control Key at the same time as the Shift Key alters
175
the behaviour of the mouse drag action such that the zoom box always
extends over the current mass range, but permits the height of the box to be
ĚĞƚĞƌŵŝŶĞĚĨƌŽŵƚŚĞĐƵƌƐŽƌ͛ƐĨŝŶĂůƉŽƐŝƚŝŽŶ͘
To perform the zoom action, click inside the zoom box.

While zoom-actions permit a global perspective of a spectrum to be
transformed into the display of a specific peak, there is always a cost
associated with mouse actions required when transforming the display to see
the peaks located at a nominal mass. The problem lies in the sparse nature of
the mass peaks compared to the number of data bins comprising a spectrum.
It is for this reason that the nominal masses can be broken down into
individual VAMAS blocks using the Display Linked VBs button on the Element
Table property page described above, thus offering a means of individually
displaying a user defined set of VAMAS blocks. When these blocks are
displayed, each spectrum appears such that the intensity scale is appropriate
for each and every VAMAS block. However, while ensuring the peak
structures are visible, the relative scale of these data, when viewed as
individually scaled tiles, is lost. For this reason new SIMS toolbar buttons
are introduced to permit the intensity scale for the entire set of data
displayed in the left-hand pane of an experiment frame to be determined
from the active tile. These toolbar buttons when coupled with the extension
to the number of tiles per row, from four to ten, allows the peak structures
176
within each VAMAS block to be visualized with a similar perspective of

intensity as that seen in an overlaid plot of the data. The following display
shows two rows of VAMAS blocks after scaling with respect to the tile with
heading 43.
The Page Tile Format dialog window provides the means of adjusting the
number of tiles per row and the Tile Display Parameter dialog window offers
display settings for switching the tile display to those seen. The organization
of the VAMAS blocks in the scrolled list means that paging down the scroll list
effectively scrolls through the mass range in the spectrum being displayed.
The enhanced Page Tile Format window provides the means of changing
the number of tiles per scroll position in the left-hand pane of the
experiment frame.
177
To display the VAMAS blocks without an x-axis, the Tile Display Parameters
dialog window is used.
Profiling Features for ToF data
Figure 28 ToF Mass Spectrum displayed using Time Bins. Data provided by Prof. Winograd,
Pennsylvania State University, USA.
ToF MS is often categorized according to the method for generating the ions
from the sample. The data in Figure 28 is an example of Secondary Ion Mass
Spectrometry SIMS, where the ToF technique is used to separate ions with
different mass-to-charge ratio following exposing the sample to a focused
beam of ions from an ion gun. Since the beam from the ion-gun can be
scanned across the sample surface, ToF data may be collected over a set of
points on the sample. Knowledge of where on the sample a time event was
recorded allows the spectral data in Figure 28 to be assigned to pixels in mass
resolved images as seen in Figure 29. These images in Figure 29 correspond
178
to the peaks identified in Figure 28, that is, each image is obtained by only
counting time-events contributing to the peaks labelled on the spectrum.
Figure 29: Mass resolved images extracted from the ToF SIMS data file corresponding to the
histogram Figure 28.
Similarly, identifying pixels in an image and only counting time-events

corresponding to the selected pixels permits multiple spectra to be extracted
from a single ToF data file. Given the complex nature of ToF spectra, the
ability to retrospectively examine the data from an experiment is a powerful
tool in understanding the information in the spectra.
ToF MS is used to obtain spectra through ionization mechanisms other than
SIMS. Proton Transfer Reactor (PTR) ToF MS (Figure 30) provides a soft
ionization mechanism of an analyte by the transfer of a proton from H3O+ to
the analyte. While spatial information is not appropriate for PTR ToF MS, the
technique provides temporally separation of spectra, where variation of
mass-peaks with time provides a profile (Figure 31) of changes in a sample.
Figure 30: Schematic of a PTR ToF MS (Kore Technology Limited, UK)

179
The tools for the purpose of visualizing the data from a ToF MS experiment
are described in following sections.
ToF Data File Options
The options on the SIMS toolbar for manipulating ToF MS data fall into two
categories: those for which a new VAMAS file is created without reference to
other data and those for which an existing spectrum or image is used to
create spectra or images representing a subset of the data within a file.
Figure 31: A profile of PTR ToF MS peaks.
Currently, two types of file formats may be processed using these options:
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University) Bio ToF XYT files. Both types of files contain time information as
well as associating the time information with image pixels.
The first step to viewing a data file is to create a spectrum from the entire file
of time values regardless of whether the file is a set of images or a profile of
some description. From the total spectrum, peaks are identified from which
180
images or profiles are created. In turn, the images or profiles can be used to
define the pixels or layers of interest, which once specified are used to extra
pixel or layer filtered spectra from the original data file.
Create a Total Ion Spectrum

A total ion spectrum is created from a data file specified using the resulting
File Dialog window shown in Figure 32.
Figure 32: Convert to VAMAS File Dialog window used to specify the ToF MS files.
The file types supported are:

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MS instruments. The lst files contain a list of binary data in which each
analysis ToF cycle appears as a sequence of start events followed by a list of
stop events representing ions arriving at the detector. While these analysis
cycles may be associated with a pixel in an image or a layer of a profile, the
spectrum created from the lst file ignores these distinctions and generates a
single time histogram from the timing information. Images or profiles are
subsequently generating from the list file using the total spectrum as a
reference.
ϮͿ&ŝůĞƐǁŝƚŚƚŚĞĞǆƚĞŶƐŝŽŶ͞ǆǇƚ͟ĐƌĞĂƚĞĚĨƌŽŵƚŚĞWĞŶŶ^ƚĂƚĞhŶŝǀĞƌƐŝƚǇŝŽ
ToF instrument. The xyt files are binary files containing a two dimensional
array of lists, where each pixel in an image is associated with a list of stop
events specifying the arrival times of ions at the detector. The total ion
spectrum is created by ignoring the spatial information and generating a
histogram from the entire set of time lists.
3) Files with the extenƐŝŽŶ ͞ƐƉĐ͟ ŐĞŶĞƌĂƚĞĚ ĨƌŽŵ ƚŚĞ <ŽƌĞ dĞĐŚŶŽůŽŐǇ >ƚĚ
instruments. These spc files are already in the form of a time binned
181
histogram. No image or profile information is present in these files. Sets of

spc files within a directory can be profiles using the options below.
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Bio ToF instrument. The dat files are already in the format of a time binned
histogram. No image or profile information is present in these files. Sets of
dat files within a directory can be profiles using the options below.
Creating a time spectrum from a raw data file involves selecting the file
with the appropriate file extension using the File Dialog window shown in
Figure 32. Once a file is converted and displayed in an experiment frame, the
data can be selectively processed using information defined on the total ion
spectrum.
Figure 33: Total Ion Spectrum from an Image File.
The spectrum in Figure 33 is a total ion histogram which is mass calibrated

and prepared with quantification regions in anticipation of processing a set of
images from the raw list file. The quantification regions define the time
intervals over which ions are allocated to pixels in images as the list file is
processed a second time. Figure 34 represents the outcome to the second
pass through the list file; the images are obtained from the second pass by
only collecting and allocating counts to images in accordance with the
quantification regions define on the spectrum in Figure 33.
182
Figure 34: Images processed from the list file corresponding to Figure 33.
The steps taken to create these images will now be described.

Create Images from Spectra using Quantification Regions
Once a total ion spectrum is available, the data can be mass calibrated using
one of two procedures: 1) define a set of calibration points in the form of
(time, mass) pairs via the Exact Mass Calculator on the Element Library dialog
window or 2) define a set of calibration regions using the Quantification
Parameters dialog window and calibrate the spectrum using a button from
the SIMS toolbar. While it is not necessary to calibrate the time bin spectrum
before generating images, given a time-to-mass calibration the automatic
region creation option on the Element Library dialog window will assign the
nominal mass to the region names and therefore aids the interpretation of
the data.
Defining Quantification Regions using the Find Peak buttons

Regions defined on the total ion spectrum provide the time intervals over
which counts are accumulated into images. The Quantification parameters
dialog window permits regions to be created one at a time, however ToF MS
is typically blessed with numerous peaks and creating a region for each of
these peaks manually would be too time-consuming. As a result, the Element
183
Table and Periodic Table property pages offer Find Peak buttons, which for
ToF data will create a region for each peak subject to a threshold criterion.
While the regions are created by simply pressing the Find Peaks button on
the Element Table property page, it is worth reviewing the limits of the
regions using the Reset and Zoom Out toolbar buttons. When the
Reset button is pressed, any regions created on a spectrum are loaded onto
the zoom-list. Thus pressing Reset followed by repeatedly pressing the Zoom
Out button will step through the regions created by the Find Peaks button.
The limits for the regions can be adjusted under mouse control provided the
Region property page is visible on the Quantification Parameters dialog
window.
Creating the Images

The total ion spectrum retains a record on the file from which it originated,
therefore pressing the toolbar button with toolbar hint List File to Images
will cause the original list-file to be scanned a further time. During the second
scan of the list file, counts are accumulated into images defined by the
current set of regions on the spectrum displayed in the active tile. Note,
regions created automatically may be numerous and therefore the resulting
image data file is potentially large. The operation is similarly potentially time
consuming and may take several tens of seconds, depending on: the number
184
of regions as well as the processor power, memory and disk speed of the PC
performing the operation.
The spectrum in Figure 33 was used to create the images displayed in Figure
34 via the toolbar button.
Spectra Generated from Image Zones
Given an image of the sample, a false colour scale defined over intensity
ranges offer a means of specifying which pixels from the image should be
included in the procedure for creating time-bin histograms from the list file.
As a result, one or more spectra can be extracted from the list file which will
be referred to as LUT spectra (Look-Up Table); the colour used to display a
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values.
The image in Figure 35 is an example of a mass resolved image displayed
using a false-colour-scale consisting of four colours. The intensity scale is
partitioned into the false colours defined using intensity ranges characteristic
of the implanted gallium lettering PSU and the complementary pixels to the
gallium lettering. Four spectra are generated from the list file based on the
four false colours defined on the image by only collecting time events
corresponding to the pixels displayed using the false colours. A comparison of
these LUT spectra for the gallium mass range is made in Figure 36.
Figure 35
The procedure for generating LUT spectra is as follows:
185
1. Select an image generated from the original total ion spectrum for a
list file.
2. On the Image Processing dialog window, available from the Options
menu, select the Colour Scales property page.
Figure 36
3. Select the False radio button from the Scale Type list and press the
Apply button.
186
4. Mark a range on the image colour scale displayed next to the image in
the left-hand-side of the experiment frame using the cursor whilst
holding down the left-mouse-button.
5. Press the button labelled Add False Colour. The colours, as specified by
the dialog window which appears when the button is pressed, are
displayed in the colour scale in the active tile and the image itself is
updated using the newly define false colour.
The default false colours are ordered to agree with the colours used to
display spectra when overlaid in a tile.
6. Once the desired zones of pixels are assigned false colours, the image
can be made the current template using the Define Image on the
Image Processing property page.
7. To generate the LUT spectra press the toolbar button. The list file
corresponding to the image is scanned and, for each false colour in the
image defined by the previous step, a spectrum is added to a new
experiment frame.
Creating a Profile from a Total Ion Spectrum

The concept of a ToF list-file is applicable to time dependent measurements
where spectra evolve during the course of an experiment. The data from
such an experiment can be treated as a total ion spectrum. Just as the data
from an image can be interpreted as a large area analysis to produce a single
spectrum from all the data, so too can all the ToF timing information be
interpreted as a single spectrum; the difference being that, in creating the
total ion spectrum the for a profile, all the changes over time are ignored.
187
Figure 37: PTR ToF MS total ion data showing quantification regions prepared for the
purpose of creating time-dependent intensity profiles.
The total ion spectrum in Figure37 provides a coarse description of the

experiment, from which the time dependent information can be extracted.
The procedure used to plot the variation of the spectra with time is similar to
that of extracting images from an image list file, that is, quantification regions
are assigned to the mass-peaks on the total ion spectrum followed by
pressing the toolbar button. The total ion spectrum maintains a reference
to the original list-file, therefore on pressing the toolbar button, the list-file is
scanned a second time producing a trace for each quantification region
defined on the total ion spectrum.
Figure 38: A plot of three traces from the regions defined on the total ion spectrum in Figure
37.
188
The data in Figure 38 represents three quantification regions from the

regions defined on the total ion spectrum in Figure 37. The oscillations in the
profiles are due to changes in the air sampled from a subject whilst the
mastication of food is performed.
Spectra Generated from Profile Layers
Figure 39: Spectra generated from the regions defined on the profile in Figure 38.
Given a profile such as the one on Figure 38, spectra corresponding to a

range of times or cycles can be generated as illustrated in Figure 39. For each
quantification region defined on a profile, (Figure 38 includes two such
regions) a spectrum is obtained by summing only those times falling into the
ranges specified by the regions.
Quantification regions are added to a profile using the Quantification
Parameter dialog window. Given the two regions in Figure 38, pressing the
toolbar button causes the list-file to be read a further time accumulating
the spectra from the timing data. The spectra in Figure 39 are examples of
data collected from layers within a profile experiment.
Create a Profile from a Directory of Files

So far, ToF list files have been considered as the data structure managing
images of spectra or profiles of spectra. The extension to the concept of a list
189
file is a directory of list files, where each list file represents a change in terms
of the experiment performed. For example a depth profile of image list files
offers the possibility of measuring an image of spectra for each layer within a
sputter depth profile. The experimental conditions evolving during the course
of the experiment are the depth beneath the surface at which an image of
spectra is acquired. Such experiments are by nature time consuming and
large in data size.
Creating a profile from a directory of list files involves selecting a
representative spectrum from the directory of list files suitable for specifying
the mass calibration and also the set of peaks to be profiled throughout the
directory of files.
The active tile must display a spectrum for which regions are defined suitable
for mass calibration. Once the spectrum is prepared the process is initiated
via the toolbar button. A File Dialog window allows the specification of a
data directory containing the files for which the list files are processed as
follows:
1. Converted to spectrum VAMAS files.
2. Each spectrum is mass calibrated using the regions defined on the
spectrum in the active tile.
3. Peaks identified using an automatic threshold search and regions
created for each of these peaks identified.
4. The region intensities are collected into profile traces for each region
created in the peak identification step.
5. A new experiment frame created using the name specified on the File
dialog window.
Initially the directory of list files appears as follows.
190
Each file with the directory is processed during the course of the profile
procedure. On completion, the same directory appears with a VAMAS file
corresponding to each original list file plus one further VAMAS file containing
the profile traces for each peak identified as significant. After processing the
directory appears as follows.
Before pressing the Profile from Files toolbar button, a spectrum must be
displayed in the active tile prepared with regions sufficient to provide an
adequate mass calibration.
The file name for the profile with the appropriate list-file extension, entered
in the Filename text-field on the File dialog window, specifies the type of list
files in the current directory and on pressing the Open button, the profiling
191
operation is initiated. These files tend to be large; therefore the time taken to
complete the profiling task may be large too.
When the profile is complete, a new experiment frame opens in CasaXPS and
the profile traces are displayed. A typical profile file will contain numerous
profile traces.
Convert and Merge a Directory of XYT File

An alternative to automatic profiling a directory of list files is to analyses the
depth profile using the set of total-ion spectra converted from each XYT file
in a directory.
A profile experiment, in which a sequence of images is acquired into separate

XYT files, can be investigated in terms of the total ion spectra using the
toolbar button. A File Dialog window is used to specify both the directory
containing the XYT files and the name of the file created by scanning the
directory for XYT files; the XYT files are individually converting into VAMAS
files containing the total ion spectra. After each XYT file in the directory is
converted, the set of VAMAS files are merged into a new experiment frame.
192
Figure 40: Merged XYT files
To load a directory of XYT files into a new experiment frame, select the
toolbar button to invoke a File Dialog window; move to the directory
containing the XYT files then enter a name into the file name text-field with
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memory, therefore take care not to attempt to merge an excessive number
of file as the operation may take considerable time to complete.
Once a set of spectra are loaded into an experiment frame, trends within the
data can be assessed using the Custom Report mechanism on the Report
Spec property page of the Quantification Parameters dialog window shown in
Figure 40. A set of profiles determined from the data in Figure 40 are
displayed in Figure 41. These profiles are obtained by defining a set of
quantification regions using the Regions property page, generating an Area
Report using the Custom Report on the Report Spec property page then
creating a new VAMAS file from the tabulated report via the Create Profile
menu option on the File menu.
193
Figure 41: Profiles generated from the merged spectra shown in Figure 40.
Image Depth Profile Data Analysis

Given a directory of xyt files:
Create an experiment frame containing a profile set of images
corresponding to the set of regions defined on a spectrum in the active tile.
Figure 42: Set of images created by accumulating counts into pixels based on regions defined
on a spectrum.
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Figure 43: Spectrum used to create images in Figure 42.
The images displayed in Figure 42 were generated from a directory of XYT

files, where data from the XYT files are processed only for those counts falling
within the time windows specified by regions defined on the associated
spectrum in Figure 43.
Three regions were defined using a total ion spectrum. The spectrum must be
displayed in the active tile before pressing the toolbar button. The
operation involves reading the entire set of XYT files in the directory specified
via the File Dialog window. The process is potentially time consuming. To
process a directory of XYT files, a file name must be specified in the File name
text-field on the File Dialog with extension .xyt. On completion, a new VAMAS
file is created with the name specified concatenated with the .vms file
extension.
Figure 44: False colour image used to generate profiles in Figure 45.
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The Image Processing dialog window on the Options menu offers tools for
processing these sets of images. For example, the false colour image scale
defined on the image displayed in Figure 44 may be used to generate depth
profiles for the sum of pixel based on coloured zones.
Figure 45: Profiles constructed from a directory of XYT files using the false colour image in
Figrue 44.
Creating the profiles in Figure 45 requires the generation of LUT spectra from
the directory of XYT files. Regions defined on the LUT spectra coupled with
the Custom Report on the Report Spec property page of the Quantification
Parameters dialog window provide to tools to create the profiles based on
false colours.
Figure 46: Spectra collected using the false colour image in Figure 44.
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Generating LUT Spectra from a Directory of List Files

Spectra from False Colour Zones
Given a directory of XYT files and a false colour image, the toolbar button
creates a new experiment frame containing a set of spectra from each XYT
file, where the spectra are accumulated from the time information from only
those pixels identified by the false colours in the image. For example, the
false colour image in Figure 44 is the sum of all the gallium 69 isotope images
and therefore the colour zones are determined by the gallium distributed
throughout the volume sampled by the depth profile. Spectra from these
four colour zones are collected into the new experiment frame shown in
Figure 46, thus the depth profile can be examined from the perspective of
gallium using these spectra.
Quantification Reports and ToF Data

The intensity associated with a ToF mass spectrum represent ions counted at
a detector. The time element of the measurement is less important than is
the case for other techniques where a specific data channel is monitored for
a specified time; data under these measurement conditions are typically
quantified in terms of counts per second (CPS). For ToF Data, the pulsed
extraction of ions and the delay required to allow ions to traverse the flight
tube result in a departure from the need to consider counts per second, but
rather to focus on the number of ions detected. CasaXPS generally assumes
data are quantified in terms of CPS and peak areas are integrated with
respect to the independent variable. Since the default quantification regime
in CasaXPS is not appropriate for ToF data, there are ToF motivated
configuration options to permit quantification of ToF intensities in terms of a
summation of counts over time or mass bins.
Quantification via the Report Spec Property Page

The Report Spec property page of the Quantification Parameters dialog
window offers two methods for generating quantification reports. The
Standard Report is predominantly aimed at tabulating results on a spectrum-
by-spectrum basis; while the Custom Report is designed to support the
profiling of data acquired sequentially, for example a depth profile.
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Standard Report
The Standard Report permits quantification in terms of quantification regions
and/or synthetic components. For ToF data, quantification based on number
of ions requires the specification of appropriate configuration files. These
configuration files are located in the directory called CasaXPS.DEF.
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Generating a quantification report for ToF data requires the use of ASCII
configuration files named:
Report Button Pressed Configuration File Name
Quantification Regions RegionQuantTable.txt
Synthetic Line shapes ComponentQuantTable.txt
Regions and Comps RegionComponentQuantTable.txt
The configuration files can be edited using Notepad or any other text based
editor.
The format for the files is a list of keywords entered one per line, where each
keyword specifies the type of information appearing in each column of the
text quantification report generated when the corresponding button on the
Standard Report is pressed.
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A quantification report is created for those VAMAS blocks selected on the

right-hand pane of the experiment frame with focus.
On pressing the Regions button from the Standard Report section with the
Use Config File tick-box tricked, the following report is produced:
For ToF data, the important column is the one specified using the keyword
SIMS_PEAK_AREA in the RegionQuantTable.txt configuration file. The
columns in the quantification report have a one-to-one correspondence with
the keywords entered in order one-per-line within the RegionQuantTable.txt
file.
The quantification report is exported as a tab spaced ASCII data set through
the clipboard. To move the quantification report to a spreadsheet, for
example, press the Copy button on the top toolbar. A clipboard dialog
window offers the option to save the data to file or copy the data onto the
clipboard.
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The data on the clipboard can be pasted into another program such as Excel.
Custom Report
The profiles in Figure 45 were created using quantification regions and the
Custom Report section on the Report Spec property page.
Since ToF intensities are determined from the number of ions within a peak
and not the peak area, quantification items defined on the spectra, either
regions or components, must include a keyword in the Tag field and the
report must be generated using the Tag Defined Report button. To indicate
that a region or component derives from ToFSIMS data, the keyword tofsims
must be entered in the Tag field for the quantification item.
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The Tag Defined Report button uses the keyword in the Tag field to
determine the type of data to retrieve from the quantification item. The
keyword tofsims causes the summation of the counts within the region or
under the components on a bin-by-bin basis. Other keywords include height,
which returns the maximum peak height as the measure for intensity. Note:
for both keywords tofsims and height, the intensities are divided by the value
entered in the RSF field; therefore the number of ions recorded for a given
peak is only obtained for an RSF of unity.
A further word of warning: the Custom Report is defined in terms of a list of
names and formulae. The formulae are constructed from the name fields
used to specify the quantification items. There is no difference between how
regions and components are treated within these formulae, both are
considered to be quantification items and intensities from regions and/or
components can be combined to create a quantification report. A key
property of the Custom Report is that, intensities from either regions or
components or both with the same name field are automatically summed
together. To be sure that the profile is from exactly the intended items,
always use different names for items included in the profile.
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An Overview of Working with ToF Data in CasaXPS

The SIMS toolbar is displayed via the View menu on CasaXPS.
The SIMS toolbar offers a range of options for displaying and manipulating
ToF MS data.
Display Options:
ToF Time to Mass Calibration Options:
Organization of Data:
Data Conversion Options:
SIMS Toolbar Buttons: Display Options

The toolbar button switches the display setting between forcing data to
be displayed with a lower intensity of zero and allowing a selectable lower
limit. The default state for the display of ToF MS spectra is to force a lower
limit of zero. A line is drawn at the bottom of the tile to indicate when the
display is forced to plot intensities above zero intensity. When the line
appears at the bottom of the tile displaying the ToF spectrum, a zoom box
drawn over the display will only indicate the upper limit for the purposes of
expanding the display.
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On left-clicking inside the zoom box with the zero base line active the display
becomes:
Toggles the display between log and linear display modes:
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Overlay selected VAMAS blocks by column:
Given a selection of VAMAS blocks in the right-hand pane, display each

column of VAMAS blocks in separate tiles in the left-hand pane. Each tile is
scaled with respect to the spectra displayed within the tile.
Adjust the scale for the tiles displayed in the left-hand pane with
respect to the intensity range determined from the active tile.
Adjust the scale for the tiles displayed in the left-hand pane with
respect to the intensity range currently used in the active tile and toggle the
mode for the y-axis display.
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Display state modified by the toolbar button are as follows:

Off On
Cycle the display through a set of predefined mass ranges.
A spectrum displayed in the active tile changes the mass range used to view
the data each time the toolbar button is pressed. The mass range is
always anchored by the smaller mass limit and with each press of the button
the size of the display range cycles between 5 amu, 10 amu, 25 amu, 50 amu
and 100 amu.
Step the mass range towards higher mass values or towards lower
mass values. The current mass range determines the size of the step. On
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pressing either toolbar button, the mass range is stepped by half the interval
currently being displayed.
Expand the display range about the central mass defined for
the active tile. The SIMS toolbar button increases the mass range about the
central mass for each press of the button without rescaling the intensity
range. The equivalent button on the second toolbar performs the same
operation as the SIMS toolbar button with the exception that the button on
the second toolbar also rescales the intensity range.
Step the current mass range by one amu. The intensity scale is
unaltered by pressing either of these buttons.
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Given a spectrum displayed in the active tile, the toolbar button adds a
set of tiles to the scrolled list of tiles in the left-hand pane, where the display
range in the active tile is split into sub-ranges, the number of which is define
on the dialog window invoked by the toolbar button. The display before
pressing the toolbar button:
Result of splitting the full spectrum into eight sub-ranges, one per tile is
shown below:
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Each sub-range is rescaled within the display tile. Note that if the number of
tiles exceeds the number of tiles-per-page in the left-hand pane, the
additional tiles cause the scroll-list to expand indicating the existence of
further pages of display tiles.
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SNMS in CasaXPS
An Overview
Sputtered Neutrals Mass Spectrometry (SNMS), as a technique related to
SIMS, is supported on the Dynamic SIMS dialog window of CasaXPS.
The Dynamic SIMS property page is available from the SIMS toolbar
The SIMS toolbar is displayed using the View menu on the CasaXPS Main
Window menu bar.
Quantification of SNMS profiles requires the calculation of sensitivity factors.

These SFs are calculated using options on the SNMS RSF Calculator property
page.
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Relative SFs are SFs normalised with respect to a given isotope. Both SFs and
RSFs are determined based on measurements from standard materials. Once
established for a set of isotopes, data measured under identical conditions
can be quantified in terms of either Atomic concentration or Mass
concentration using options on the SNMS RSF Calculator property page.
Further tools for transferring RSFs to other measurements are available on
the Prepare Profile property page.
The function of the Prepare Profile property page is to copy RSF and sputter-
rates to multiple data files with the view to generating quantified profiles
from the raw SNMS data. The buttons on the Prepare Profile property page
are designed to work based on selections made within the set of opened
files. To this end, other buttons on the Prepare Profile property page provide
a means to make selections appropriate for the action buttons.
SNMS and Dynamic SIMS are specified in CasaXPS using an identical
framework. The RSF and sputter-rates are assigned on a measurement-cycle
by measurement-cycle basis. In both SNMS and Dynamic SIMS, a profile fully
prepared for quantification must have each cycle populated with RSF and
sputter-rates as viewed via the Calibration property page of the Dynamic
SIMS dialog window.
The sputter-rate for a given profile is calculated using the Calibration
property page and, using the same mechanisms as for Dynamic SIMS, the
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sputter-rate and appropriate RSF entries are updated. The table on the
Calibration property page displays the parameters used during quantification.
Basics of CasaXPS
Converting Data
CasaXPS native file format is ISO 14976 VAMAS file. CasaXPS contains many
conversion filters available from the Convert menu option on the File menu
or via the top toolbar.
Converting data involves selecting the data file with the appropriate file
extension via the Convert to VAMAS file dialog window.
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For example, Hiden data is saved in comma separated format with file
extension csv. On selecting a file containing Hiden data format with the
extension csv, CasaXPS will convert the data to VAMAS format and write a
new file into the same directory as the original csv file.
The VAMAS file will then open as an Experiment Frame in CasaXPS.
Data Viewed Via an Experiment Frame

A profile experiment contains one or more traces measured and recorded for
each isotope monitored. The Experiment Frame in CasaXPS displays the data
using two panes with an adjustable central divider.
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The left-hand-pane displays the data in graphical form.
The right-hand pane offers the data blocks within the VAMAS file.
The right-hand pane is used to make selections from the set of VAMAS blocks
held within the VAMAS file. These selections are used to display subsets of
data within the file and direct processing operations to specific data blocks.
Displaying Data
Individual VAMAS blocks appearing in the right-hand pane are displayed by
double-clicking the left-hand-mouse button with the cursor over the data
block.
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Selecting more than one VAMAS block in the right-hand pane and using the
Overlay toolbar button causes the selected VAMAS blocks to be displayed in
the active display tile.
Selecting VAMAS Blocks

Selections are made using the right-hand pane:
1. Single click the left mouse button over the right-hand pane to select a
single block of data.
2. Hold the Shift-Key down and single click the left mouse button over a
different block in the right-hand pane to make a range selection.
3. To add to or remove from the current set of selected VAMAS blocks,

hold the Control-Key down before left clicking the mouse with the
cursor over a VAMAS block in the right-hand pane.
4. Use the Select menu to extend a selection to other VAMAS blocks of
similar identity in other files.
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Tile Display Options

The left-hand pane of an Experiment Frame displays the data in the form of
profiles, spectra or images. Options affecting the display are managed using
the Tile Display Parameters dialog window. The Tile Display Parameters
dialog window is invoked via the top toolbar or from the

Options menu
When plotting a profile involving multiple traces, a common requirement is

to place a Legend or Key within the tile in which the data are plotted. The
Display property page on the Tile Parameter dialog window provides control
over placing a Key on either the right-hand side of the graph area or
alternatively the left side via the Draw Key and Key on Left tick-boxes.
216
The Display property page also allows the profiles to be plotted using lines,
points or both lines and points.
Display Colours
The colours used to plot the profiles are specifies using the Colours property
page on the Tile Display Parameters dialog window.
To modify the colours used to display the profiles, press the button on the
Colours property page on the Tile Display Parameters dialog window labelled
Spectra. Use the Colour dialog window to adjust the Custom Colours palette
217
before pressing the OK button on the Colour dialog window followed by

Apply or OK on the Tile Display Parameters dialog.
The order for the colours used to display the profiles is determined by the
Custom Colours moving left to right then top to bottom as view on the
Colours dialog window. Further, the order of the VAMAS blocks displayed in
the Active Tile is determined by the order in which the data blocks are
selected in the right-hand pane.
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Holding the Control Key down allows the order of the data blocks to change
and therefore the colours change accordingly.
Calculating SNMS Sensitivity Factors

The task of calculating a set of sensitivity factors for SNMS requires a
standard sample of known composition and a measurement from the
standard sample, where a specific set of isotopes for which sensitivity factors
are to be determined is used to monitor the sample-composition in terms of
counts per second. The SNMS RSF Calculator determines a set of factors
relating the amount of substance to the signal measured. Thus these
sensitivity factors provide the scaling factors to convert measured signal to
amount of substance for profiles measured from samples of unknown
material composition. The calculation of SNMS sensitivity factors is
performed using the SNMS RSF Calculator property page on the Dynamic
SIMS dialog window.
219
An example of a standard sample is a Hastelloy material for which the

composition is known to be:
Element % Composition by
Weight
Cu 0.2
Ni 51.5
Cr 16.15
V 0.22
Mo 17.1
Co 1.5
W 4.29
Fe 7.3
When measured using a quadrupole mass spectrometer, the recorded signal
from the Hastelloy sample defines the instrumental response for the given
sample composition.
220
Armed with the experimental data measured from the standard and the table
of material compositions, the sensitivity factors for the isotopes used in the
experiment are calculated by populating the table on the SNMS RSF
Calculator property page and defining a quantification region for each
VAMAS block. The quantification region provides a means of estimating
representative signal intensity for each profile.
The information used to calculate the sensitivity factors is recorded in the

VAMAS blocks for each of the profiles. It is therefore necessary to update the
appropriate information for each of the VAMAS blocks representing the data
measured from the standard sample.
To update the information needed to compute the sensitivity factors, repeat

the following steps for each isotope in the SNMS profile measured from the
standard sample.
1. Double-click a VAMAS block in the right-hand pane.
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2. Select the type of percentage known about the composition of the

sample and enter the value for the percentage in the text-field.
The Update Value button becomes active as soon as a value is entered for the
percentage composition.
3. Check that the correct mass per mole and isotopic mass are displayed
and press the Update Value button.
The table on the property page displays the values currently available for
profiles displayed in the active tile.
The mass per mole is determined from the average mass for a given element,
while the isotopic mass represents the mass of the peak used to measure the
profile signal.
The table is only updated when the Update Values button is pressed.
222
Each VAMAS block holding the data from a profile must be updated with the
composition information. Overlaying the VAMAS blocks for the full profile in
the active tile causes the table on the SNMS RSF Calculator to display the full
list of quantification information.
The table reflects the percentage composition for the standard sample. To
relate these percentage compositions to the signal intensities for the set of
profiles, it is necessary to specify a representative intensity for each isotope.
The representative intensity is determined as the average over a set of
acquisition cycles as specified via a quantification region. Specifically, the
signal intensity is the average intensity over the set of data cycles defined by
the first quantification region for each VAMAS block in the experiment.
4. Create a quantification region for each VAMAS block, where the limits
to the region define a set of data channels over which the intensity can
be averaged and assumed to be representative of the signal measured
for the isotope being profiled.
The quickest means of creating quantification regions on SNMS/SIMS data is

to use the Calibration property page on the Dynamic SIMS dialog window.
223
Overlay all the VAMAS blocks in the active tile before pressing the Define
Surf/BG button on the Calibration property page.
224
The Define Surf/BG button creates two quantification regions per VAMAS
block overlaid in the active tile. Only the first region, assigned the name Peak,
is used to determine the signal intensity for the SNMS data. The reason two
regions are created is to allow dynamic SIMS experiments to define a surface
zone and a zone representative of the background signal to a SIMS profile.
The quantification regions are so named because of their use in XPS data
analysis. For the purposes of SIMS and SNMS, the regions only define
intervals. Should these intervals need changing from the default values
obtained by pressing the Define Surf/BG button, the Regions property page
on the Quantification Parameters dialog window provides a means of making
changes to these interval limits.
Each VAMAS block must be updated with any changes to the region limits.
Quantification regions are propagated from one VAMAS block to others by
selecting the range of VAMAS blocks in the right-hand pane of the
experiment frame and right-clicking the mouse over the left-hand pane
displaying the data with the modified regions. A dialog window appears
offering the ability to propagate the regions to other VAMAS blocks listed on
the dialog.
225
Tick the tick-box in the propagate section and press the OK button. A further
dialog window appears requesting confirmation, which should be accepted
by pressing the Yes button.
Assuming that the background region is deleted and the Peak region adjusted
to provide a representative average signal from each profile, the appearance
of the set of profiles changes as follows.
226
Following the creation of an appropriate quantification region, the SNMS RSF

Calculator property page will show the average value determined from the
region for the first VAMAS block displayed in the active tile.
The VAMAS file for the standard sample is now ready to calculate the
sensitivity factors for the measured isotopes.
VAMAS blocks used in the calculation of the sensitivity factors must be:
1. All overlaid in the active tile
2. The table on the SNMS RSF Calculator property page displays the
correct percentage compositions , Mass per Mole and signal isotopic
mass
3. A region is defined on each VAMAS block.
Once the data are prepared appropriately, pressing the Calculate SF button
calculates and adds sensitivity factors to the table on the property page.
227
Alternatively, relative sensitivity factors are calculated by first selecting an

entry in the Name column of the table before pressing the Calculate RSFs
button .
A dialog window report the reference isotope by name and on pressing OK,
the table is populated with RSF with respect to the indicated VAMAS block.
In both cases, the RSF or SF values are also entered into the VAMAS blocks on
a cycle-by-cycle basis, which can be verified via the Calibration property page
of the Dynamic SIMS dialog window.
228
Quantification of SNMS Profiles

Isotopic profiles are quantified by applying the sensitivity factors to the
intensities measured from the sample. These sensitivity factors are
maintained within profiles measured from standard materials of known
composition. The quantification of a profile is therefore achieved by
transferring the appropriate sensitivity factors from these standard materials
to the unknown material, establishing the sputter-rate for the material under
analysis, followed by calculation of the percentage atomic or mass
concentrations. The result is a new experiment frame containing the
quantified profile. The process will be illustrated by quantifying a stainless
steel sample using sensitivity factors determined from a Hastelloy material of
known composition.
Quantification of Stainless Steel using SNMS: an Example
On conversion, the data from a stainless steel sample appears in CasaXPS,

viewed via the Calibration property page of the Dynamic SIMS dialog window,
as a set of VAMAS blocks in the right-hand pane of an experiment frame.
The Calibration property page shows that initially the profiles are all assigned
an RSF of unity and a unit sputter-rate.
229
RSFs and sputter-rates are defined on a cycle-by-cycle basis. This allows

values to be adjusted depending on the point in a profile at which the
intensities are measured. In multilayer materials permitting differing RSFs
and sputter-rates may be important; however for a uniform stainless steel
sample all cycles will be assigned the same RSFs and sputter-rates
independent of depth.
The Prepare Profile property page on the Dynamic SIMS dialog window
provides the tools for transferring RSFs and sputter-rates between profiles.
230
To transfer the RSFs from the Hastelloy standard to calibrate a stainless steel
sample:
1. Load both the Hastelloy profile (previously processed to include the
sensitivity factors) and the stainless steel profile.
Data converted from Hiden files include VAMAS fields defining the element
and species for the VAMAS blocks. While these strings are only important in
as much as profiles from the same isotopic peaks must be assigned identical
strings, the actual strings are at the users discretion. The Hiden data labels
ƚŚĞŵĂƐƐƉĞĂŬƐǁŝƚŚƚŚĞŶŽŵŝŶĂůŵĂƐƐƐƵĐŚĂƐ͞DĂƐƐϱϴ͘͟dŚĞƐĞĞůĞŵĞŶƚĂŶĚ
transition strings are used to make global selections within the set of open
VAMAS files; also the transfer of RSF and sputter-rate values is achieved via
the Prepare Profile property page based on these strings. Therefore, a
consistent assignment for these fields significantly aids the speed of data
preparation leading to quantified profiles.
2. Tile the experiment frames within CasaXPS so that the right-hand
panes can easily be seen
In this example only two files are in use so tiling the opened files using the
Window menu is relatively easy. When more files are involved, a cascade of
experiment frames can be more useful a means of monitoring the selections
within the file set.
231
3. Select the VAMAS blocks within the Hastelloy standard previously

prepared with appropriate sensitivity factors.
4. Press the button to match the selection from the
Hastelloy experiment frame throughout the opened VAMAS files.
5. Ensure that the source experiment frame is the experiment frame with
focus.
232
6. Press the button.
A dialog appears listing the set of VAMAS blocks together with the file names
from which the VAMAS blocks belong.
7. To transfer the RSF from the source file to the destination VAMAS
blocks, press the OK button on the dialog.
The key point to note is that the RSFs are copied only to those VAMAS blocks
for which the source VAMAS block element/species strings match the target
element/species strings. To force the transfer of RSF values to other VAMAS
blocks regardless of such constraints, use the button on the SNMS RSF
Calculator property page.
233
Following these operations the VAMAS blocks in stainless steel sample is

populated with RSFs from the Hastelloy standard. These values can be
viewed via the Calibration property page, where the table lists both the RSF
per cycle and also the sputter rate per cycle. The remaining step is to assign a
sputter rate for the stainless steel sample using the Calibration property
page.
Specifying the Sputter-Rate

The sputter rate for a profile is updated on the Calibration property page of
the Dynamic SIMS dialog window. The information presented on the
Calibration property page is designed for calibrating dynamic SIMS profiles.
The mechanism allows the specification of sputter rates and RSFs based on
matrix materials. Since the RSF is already added to the SNMS data via the
Prepare Profiles or SNMS RSF Calculator property pages, the RSF must be
retrieved before applying the newly calculated sputter-rate to the SNMS
profile. Note that all VAMAS blocks in the row containing the block used to
enter the sputter rate are also updated.
To update the sputter rate for a profile, perform the following steps using the
Calibration property page.
234
1. Select an entry from the Matrix Index column as shown.

2. Press the RSF button to retrieve the RSF value from the table.
3. Enter the Crater depth in the text-field just below the Depth (nm)
label before pressing the Compute Sputter Rate button.
4. Press the Apply RSF/SR to Matrix button.
Creating a Calibrated SNMS Profile

Once the set of VAMAS blocks containing the SNMS profile have been
populated with RSFs and the sputter-rate, quantification in terms of Atomic
or Mass concentrations is achieved by pressing the appropriate buttons on
the either the SNMS RSF Calculator property page or the Prepare Profile
property page.
235
These two property pages provide a means of quantifying SNMS data either
one file at a time or multiple files in one operation.
The SNMS RSF Calculator property page provides a means of quantifying the
SNMS profile in the active tile. To perform the quantification step, display
one or more VAMAS blocks in the active tile. Ensure the RSF and sputter-
rates are correctly assigned for each of the VAMAS blocks by inspecting the
table on the Calibration property page. To quantify the profile, press the %
Atomic or % Mass buttons on the SNMS RSF Calculator property page. A new
experiment frame is created containing a set of VAMAS blocks in which the
data are scaled by the sensitivity factors and offered as a percentage of the
total scaled intensities. The profiles are therefore presented in the form of an
amount of substance rather than the raw signal.
Before quantification the signal is displayed in raw counts against acquisition
cycle number.
After quantification, the data are presented in percentage of material against

depth in nanometres.
236
The alternative to performing the quantification on a file by file basis is to

prepare a set of SNMS profiles and then use the Prepare Profile property
page to quantify the data in one operation.
Sputter rates may be transferred to other profiles using the Prepare Profile
property page in an analogous way to the RSF mechanism.
When multiple VAMAS files are opened in CasaXPS and prepared with
appropriate RSF and sputter-rates, the Atomic % by File button or the Mass %
by File button may be used to quantify the profiles in each opened file for
which at least one VAMAS block is selected and the active tile displays data
from one profile in the file. The following steps lead to quantification for two
profiles.
1. Tile the experiment frames within the CasaXPS main window
237
2. Select one of the VAMAS blocks common to both profiles to be

quantified and press the Select and Display Matching Blocks button
3. Deselect the VAMAS block in the experiment frame for which no

quantification is required.
4. Press the Atomic % by File button.

5. Review the list of files displayed in the resulting dialog window and
press OK if all is well.
238
Two new experiment frames appear containing the quantified profiles from
the two files for which at least one VAMAS block is selected.
Note that:
Only files in which a VAMAS block is selected are quantified.
Each raw file contains the information required to perform the
quantification and therefore any number of different files can be
quantified at once provided the RSF and sputter-rates are prepare
appropriately and a selection includes at least one VAMAS block.
The Control-Key and the mouse can be used to add to the selection
across experiment frames, so the operation is not limited by the
functionality of the selection options on the Prepare Profile property
page.
239
Hiden SIMS/SNMS Workstation
Dynamic SIMS
The Dynamic SIMS technique etches a sample using an ion gun whilst
monitoring the signal for a set of isotopes. The resulting profile represents a
measure for the composition of the sample as a function of depth, where raw
data takes the form of counts per acquisition cycle as a function of
acquisition cycle time. These raw data are calibrated using the tools on the
Dynamic SIMS dialog window to provide profiles in terms of atomic density
plotted against depth in nanometres.
240
Quantification of SIMS data is complicated by virtue of measuring the

intensity of the secondary ions generated by the interaction of the primary
beam on the sample surface. The complexity results from the dependence of
the signal intensity on the bulk properties of the sample. That is, a change in
the material etched by the ion beam may alter the signal intensity for the
secondary ions regardless of the concentration of the element within the
surface. It is therefore important to identify the essential structure of a
sample, referred to as the matrix material, with the understanding that
should the matrix material change, both the signal intensity for mass peaks
may change as well as possible changes to the etch rate. SIMS analysis is
highly sensitive and ideal for the analysis of dopants, diffusion studies and
contamination. Quantification schemes for SIMS generally assume that the
impurity being measured is dilute (less than a few percent). Above this dilute
limit the probability of ionisation becomes dependent upon the impurity
concentration itself, as well as the chemistry of the matrix.
Notes on Dynamic SIMS RSF Calculation

Reference Signal Measured during the Course of Profile
Dynamic SIMS relative sensitivity factors (RSFs) are the means by which
measured implant signals are scaled to permit meaningful comparisons of
profile data. During the course of a measurement, the signal may change for
a variety of reasons and as a result a common practise is to measure both the
implant signal and also the matrix signal. The matrix signal provides the
experimental context for the implant signal, therefore the calculation of an
RSF from a standard sample includes the matrix signal measured in counts
per second. Since an RSF is essentially a scale factor and the matrix
monitored during the course of the profile is a sequence of measurement,
the value included in the RSF calculation is determined from an average of
the matrix acquisition cycles.
An alternative to measuring the matrix signal at the same time as the implant
is to monitor the matrix signal following the profile completion. The structure
of the experiment changes slightly when the matrix signal is determined
following the implant measurement, and since the RSF calculation for both
scenarios are generalised by the reference signal estimation following the
241
profile, the discussion of the RSF computation will be based on the more
general case.
Reference Signal Measured at End of Acquisition Cycles
d1
d2
Consider a sample created from a matrix material A implanted with a

ŵĂƚĞƌŝĂůƵƐŝŶŐĂĨůƵĞŶĐĞʔĂƚŽŵƐƉĞƌĐŵ2. If the resulting sample is profiled
using C data acquisition cycles followed by a matrix signal measurement,
where each acquisition cycle takes t seconds per cycle and the matrix signal is
measured for a further T seconds resulting in a crater of depth d cm, then the
RSF for equivalent samples can be determined as follows.
The reference signal measured during the period T corresponding to the etch
volume characterized by the depth d2 is assumed to be representative of the
matrix signal throughout the profiled volume characterized by the depth d1.
Further, the sputter rate is determined from the total depth of the crater
equal to d1+d2 divided by the total etch time. Hence d1 = td / (t+T). The RSF
for the given experiment is:
tCI A 1
RSF (1)
I B I bg C d1
where
1. IA is the matrix signal in counts per second,
2. IB is the sum of the signal from the implant over the acquisition cycles
C
IB I i in counts,
i 1
3. Ii are the counts record for the implant in each cycle and
4. Ibg is the background counts for the implant signal.
The formula for the RSF in Equation (1) is defined in terms of parameters
determined from an experiment. There are assumptions within this formula
regarding the nature of the experiment, which become clear when the
parameters are rearranged as follows:
242
RSF IA (2)
1 C Ii I bg
d1
C i 1 t
The denominator in equation (2) is an approximation to the integral of the
background subtracted implant counts per second integrated over the depth
of the profiled volume. That is:
d1
1 C Ii I bg ( I ( x) I bg )
d1 dx (3)
C i 1 t 0
t
where the approximation in Equation (1) assumes a uniform step-size ȴǆ с
d1/C for a rectangular integration scheme. If the step-size as a function of
depth changes during a calibration profile, the RSF calculated from Equation
(1) will be less representative of the measured uncalibrated implant dose.
Since the objective of calibrating an implant signal is to ensure that profiles
obtained from identical implantation conditions return identical areal
densities, or stated mathematically, integrals of the form in (3) for RSF scaled
intensities are all the same when calculated from profile data measured for
samples with identical implant dose, computation of the integral in Equation
(3) is preferable to the summation in the same Equation. Therefore, the RSF
calculation in version 2.3.15 of CasaXPS is now performed using:
RSF IA d1
(4)
( I ( x) I bg )
dx
0
t
Equation (4) better represents the nature of the dynamic SIMS RSF as a
scaling factor for adjusting implant intensities relative to a known fluence ʔ.
The inclusion of the matrix signal IA in the RSF calculation is to allow the
implant intensity to be further normalised with respect to the matrix signal as
a means of removing instrumental variations possible during the course of a
profile, or in the case of the reference signal at the end of the profile,
between different profile measurements.
Quantification of Dynamic SIMS Profiles

The options on the Calibration property page of the Dynamic SIMS dialog
window are designed to permit the analysis of samples for which the matrix
material changes in the course of the experiment. Although multilayer
243
materials are analysed using dynamic SIMS, the typical sample consists of a
single matrix and one or two impurities appearing in dilute quantities
compared to the matrix. For this reason, the first perspective of the
Calibration property page will be that of these more common and simple
samples.
Most data systems used to acquire dynamic SIMS profiles provide a means of
exporting the data in an ASCII format. These data files must be converted to
VAMAS format by CasaXPS using a very specific structure within the ISO
14976 definition. The experimental context for the dynamic SIMS profiles is
collected into a VAMAS file by CasaXPS and presented as a set of VAMAS
blocks. Each VAMAS block within a file manages the quantification
information in a set of corresponding variables (as specified by the ISO
format). The Calibration property page on the Dynamic SIMS dialog window
displays these corresponding variables in a table.
Data file supported by CasaXPS include:

1. Hiden Analytical Limited
2. Two formats for Cameca IMS instruments.
3. RBD Instruments Inc. PHI-upgrade system.
To convert a native ASCII format to VAMAS format suitable for quantification

in CasaXPS, convert the data using the Convert option on the File menu or
the Convert toolbar option .
244
Quantification of Basic Profiles

An example based on Cameca IMS-6f old ASCII format.
Converting Cameca Depth Profiles

Depth profile data from Cameca IMS-6f SIMS instruments can be exported via
ASCII formatted files. These files, when written to disk, are assigned a file
extension of .dp_ascii and, if exported from the raw data, include
experimental parameters plus two columns of X/Y pairs representing the
etch-time per cycle and the secondary ion intensity in counts per second.
CasaXPS will convert these .dp_ascii files only when the raw data is exported.
Conversion is performed using the Convert option on the File menu or via the
toolbar button. A File dialog window is invoked by these options, in which the
.dp_ascii file containing the raw data is selected and the Open button
pressed.
245
A new VAMAS file will be written to the same directory containing the
original ASCII data after which the profile appears in a new experiment frame
in CasaXPS.
When more than one profile is of interest, the data can be combined into a
single experiment frame via the Convert and Merge option on the File menu.
Again a File dialog window appears, in which each .dp_ascii file within the
current directory can be selected using the mouse and the Control Key; on
pressing the Open button on the dialog window the entire set of selected
dp_ascii files are converted to VAMAS files and the resulting files loaded into
a single experiment frame.
246
The directory containing the original dp_ascii files will also contain
corresponding VAMAS files. Since the conversion process involves writing
new VAMAS files, it is important that the directory containing the data must
have write permission and there is sufficient space on the disk to receive the
new VAMAS file.
Quantification Information
After conversion to VAMAS format, both the timing information and the
intensity units are adjusted to those used internally by CasaXPS. Most
notably, the intensity unit in the .dp_ascii file is counts per second, however
the intensity in the VAMAS file will be measured in counts per cycle and the
abscissa becomes cycle index. All the associated timing information is also
save with these abscissa and ordinates so that the calibration to depth and
atomic density can be computed later.
Mass channels used to measure the secondary ion intensity are labelled
within the .dp_ascii file using the nominal mass and the element name
abbreviation. When entered into the VAMAS file, the block identifier is
assigned the original string used to label the mass channel, however CasaXPS
attempts to extract the nominal mass and the element abbreviation for use
in the element and transition fields used by the VAMAS format. The
concatenation of these element and transition fields provides the
information used to align the VAMAS blocks within the experiment frame and
is also used to determine the isotopic abundance ratio, which in turn is used
to determine elemental from isotopic relative sensitivity factors. If the
247
element/transition fields for a profile are not correctly assigned, should the
user request elemental sensitivity factors an error message will result. In the
event that the element and transition fields do not contain the element and
isotopic information required to determine the relative abundance for an
isotope, then these fields must be edited to reflect the true isotope used to
measure the profile. To edit these fields:
1. Select the VAMAS block(s) in the right-hand pane of the experiment
frame.
2. Press the toolbar button and, on the resulting dialog window, enter
the correct element abbreviation and nominal mass for the isotope of those
VAMAS blocks in the selection.
When the information on the dialog window is accepted, the VAMAS blocks
in the right-hand pane of the experiment frame are re-organised to reflect
the new assignment.
One way to check the possible values for the element/transition entries is to
use the Exact Mass Calculator property page on the Element Library dialog
window.
ŶƚĞƌ Ă ƐƚƌŝŶŐ ƐƵĐŚ ĂƐ ͞^ŝϮϴ͟ ŝŶƚŽ ƚŚĞ ƚĞǆƚ-edit field on the Exact Mass
property page and press return or the Add Formula button. If a valid isotope
string has been entered, then the string will be entered into the scrolled list
above the text-field. Otherwise, an error dialog indicated an error occurred. If
248
elemental RSF values are desired, it is important the string above the VAMAS
block in the experiment frame is accepted by the exact mass calculator;
acceptance of a string indicates the database includes the information
necessary for the conversion of the RSF.
Calculating Relative Sensitivity Factors for Simple SIMS Measurements

Quantification of dynamic SIMS profiles is based on determining absolute
scaling factors, which when applied to the profile data convert the raw signal
into atom density measured in atoms per cm3. Determination of these RSFs
requires the measurement of a profile from a material of known
composition. For dynamic SIMS, known composition means knowledge of the
matrix material and the impurity implant dose used to prepare the standard.
The example used to illustrate the process for calculating an RSF is gallium
implanted with silicon (dose = 2e14 atoms per cm2, crater depth = 1776.4
nm). The profile measured on a Cameca IMS-6f includes the isotopes Ga 69
and Si 28.
The following steps lead to calibrated depth and intensity scales for the data
in the original .dp_ascii file.
249
1. Convert the .dp_ascii file using the Convert option on the File
menu.
2. Display the 69Ga data in the active display tile
3. Left-click on the active tile to enable the toolbar buttons.
4. Invoke the Dynamic SIMS Calibration dialog window by pressing the

Dynamic SIMS toolbar button .
The top left-most text-field displays the Block Id for the data which is the
current focus of the Dynamic SIMS dialog window.
250
5. Press the Define Matrix button.
Provided no cycles are selected in the scrolled list below the Define Matrix
button, a dialog window indicates that no selection is active and asks
whether all cycles should be updated for the profile in the active tile.
6. Press the Yes button and observe that the Matrix Index column of
the scrolled list is updated with the string 69Ga.
If a cycle selection has been made within the scrolled list, then all cycles must
be selected before pressing the Define Matrix button is pressed.
The second column in the scrolled list is labelled Interface. For this particular
profile, the same matrix is present throughout the etch cycles and therefore
the use of the Interface column is unnecessary. If the material were a
multilayer sample, where RSF and sputter-rates varied between layers, then
251
the Interface column would need to be populated with strings corresponding

to the different materials characterising the layer structure. Once the layers
are established, the Interface definition allows the assignment of RSF and
sputter-rates to the individual layers.
7. Double-click on the 28Si VAMAS block so that the silicon profile is
displayed in the Active Tile.
8. Press the Define Surf/BG button.

Two regions are created on the 28Si profile and these mark the surface limit
and the background to the secondary ion signal.
252
Adjustments to these regions are performed using the Quantification

Parameters dialog window.
9. On the Calibration property page, enter the crater depth value
measured for the standard (crater depth = 1776.4 nm)
10.Press the Compute Sputter Rate button.
11.On the Calibration property page, enter the dose value known for
the standard (dose = 2e14 atoms per cm2)
253
12.Press the buttons labelled Compute RSF
13.Select one cycle in the scrolled list on the Dynamic SIMS dialog
window and press the Apply RSF/SR to Matrix button.
The values from the two text-fields for the RSF and the sputter-rate will be
entered into the corresponding fields in the scrolled-list for each cycle for
which the matrix index is identical to the one previously selected.
254
14.Press the button labelled Calibrate Depth Profile.
The RSF and sputter-rate entered into the 28Si table are used to compute the
atomic density and the depth; the computed profiles are entered into a new
experiment frame.
255
The new experiment frame contains a VAMAS block for each VAMAS block in
the original file. Within these new VAMAS blocks, several corresponding
variables are defined which are assigned values for the intensity in counts per
second plus the RSF and sputter-rate used to calibrate the profile. These
values can be viewed using the Crtl PageUp/Crtl PageDown mechanism for
stepping through the corresponding variables in a VAMAS block.
NB: To compute the elemental RSF from an isotope profile, the tick-box
labelled Elemental RSF must be ticked and the element/transition field for
the VAMAS block in use must be set appropriately.
Making Adjustments to the Sputter Rate

A depth profile prepared for calibration must have an RSF and sputter rate
defined for each matrix within the analysis volume. If at a later time it is
desired to alter the RSF or sputter rate for a given matrix, the following
sequence of steps should be used:
1. Select a cycle from the scrolled-list to identify the matrix for which
the RSF or sputter-rate requires adjusting.
2. Press the pushbutton labelled Restore RSF/SR.
The values for the matrix identified by the chosen cycle are entered into the
corresponding text-fields for the RSF and Sputter Rate on the dialog window.
3. Either the RSF, the sputter rate or both the RSF and the sputter rate
can be recalculated before again pressing the Apply RSF/SR to
Matrix button. The matrix defined by the selected cycle will be
updated with the modified values.
256
Display of Calibrated Profiles

The labels for identifying the x and y axes in a display tile are determined
from the first VAMAS block with respect to the order of selection in the right-
hand pane of the experiment frame at the time the VAMAS blocks are
overlaid in the display tile. If a row of VAMAS blocks are selected by clicking
on the experimental-variable value for the row, then the left-most VAMAS
block will determine the axes labels. Matrix signals are typically not
calibrated and in the event the first VAMAS block contains the matrix signal,
the profile would appear with the y-axis displaying an arbitrary scale.
When calibration is performed, only those profiles for which quantification

information is supplied are converted to atom density. Profiles with an RSF of
unity are scaled to ensure the profiles appear within the range for the
calibrated profiles; hence the y-ĂǆŝƐ ůĂďĞů ŝƐ ĂƐƐŝŐŶĞĚ ƚŚĞ ƐƚƌŝŶŐ ͞ƌďŝƚƌĂƌǇ
hŶŝƚƐ͘͟dŽĚŝƐƉůĂǇĂŶŽǀĞƌůĂǇŽĨƚŚĞƉƌŽĨŝůĞƐǁŚĞƌĞƚŚĞzĂǆŝƐŝƐůĂďĞůůĞĚǁŝƚŚ
respect to a calibrated profile, naŵĞůǇ͞ƚŽŵŝĐĞŶƐŝƚǇ͕͟ŝƚŝƐŶĞĐĞƐƐĂƌǇƚŚĂƚĂ
calibrated VAMAS block is selected first. To select VAMAS block in an
arbitrary order, left-click the first VAMAS block, then hold the Control Key
down and left click the other blocks required for the display. The traces are
displayed in the active tile by pressing the overlay toolbar button and are
ordered with respect to the selection sequence.
257
The VAMAS block for the impurity 28Si is selected before the matrix 69Ga.
Further Aspects of Dynamic SIMS Quantification

Logical Structure of a SIMS Depth Profile within CasaXPS
A depth profile is a collection of VAMAS block all assigned to the same
experimental variable value; typically the experimental variable will be an
index number for a given file of data. There may be more than one profile per
VAMAS file, where each profile will occupy a row as viewed via the right hand
pane of the experiment frame.
258
For each VAMAS block within a raw depth profile, a number of corresponding
variables are setup to offer fields for use in the quantification step. The
important fields for quantification are displayed in the Matrix Index table on
the Calibration property page of the Dynamic SIMS dialog window.
Methods for Computation of RSF and Sputter Rate Values

RSF values are computed from standard materials using one of three
approaches:
1. Matrix, dopant and crater depth.
2. Matrix, known bulk doped atomic density and crater depth.
3. Interface assignment with respect to depth and atomic density.
The computation of the RSF requires the determination of values from the
Matrix signal and also the Implant. To support the determination of these
quantities the matrices within a profile must be identified and a pair of
regions defined to specify the surface zone as well as the appropriate
background signal for a given mass.
Identification of the Matrix and Interface Cycles

Defining the matrix for experiments involving a Single matrix material is
achieved as follows:
1. Display the matrix signal for each profile in the active display tile.
2. Press the Define Matrix button on the Calibration property page on
the Dynamic SIMS dialog window.
259
A pop-up window will inform you that no matrix index is selected and asks
whether the displayed matrix should be applied to all Cycles. Answer by
pressing the Yes button. To avoid the warning message, before pressing the
Define Matrix push button, first select all the table entries by pressing the
header button for the column labelled Matrix Index. If there are any rows
currently selected it will be necessary to de-select these rows before pressing
the header Matrix Index.
If the file contains more than one depth profile and the matrix for each
profile is overlaid in the active tile, then the operation of defining the matrix
for each depth profile is performed in one go.
Defining the matrix for Layered materials is achieved as follows:
A key point for SIMS is that the signal from a given mass peak depends on the
environment in which the isotope is found. As the crater bottom moves
through an interface between differing materials there is potential for both
the relative sensitivity and the etch rate to change during the course of the
acquisition. The example used to illustrate a layered material involves
profiling magnesium in gallium with an aluminium layer in the form of GaN :
AlGaN : GaN (Dr Shadi Shahedipour, University of Albany, New York).
The secondary ion yield for Mg differs between the GaN and the AlGaN
layers. Presentation of these types of samples requires a means of adjusting
the Mg RSF for acquisition cycles depending on the aluminium signal
strength.
The table on the Calibration property page provides two columns headed
Matrix Index and Interface. These columns specify the matrix material and
260
also structures within the profile where the RSFs for a given isotope change
due the material environment rather than changes to the atomic density. The
procedures for defining the matrix and also a layer are identical except for
different buttons are used to make the assignment. For the current example,
the Ga2 signal is most representative of the gallium matrix, while the Al signal
best defines the interface between the GaN and AlGaN layers. The matrix
signal Ga2 is common to both layers therefore the Ga2 profile can be defined
as the matrix throughout the profile:
1. Display the Ga2 VAMAS block in the active tile.
2. Ensure the Matrix Index column of the table on the Calibration

property page is either all selected or none are selected before
pressing the Define Matrix button.
261
All VAMAS blocks from the same row in the right-hand pane will now show
the same Ga2[2] matrix for each cycle throughout the profile.
At this point the Interface column is populated with the 69Ga[0] reference,
that is, the matrix and interface columns are initialised to the first VAMAS
block in the file. Only the matrix has so far been replaced by a reference to
the Ga2[2] VAMAS block. Since the depth profile includes two environments
from which the Mg signal is measured, to distinguish between these two
environments the cycles corresponding to the AlGaN layer must be identified.
The Al signal provides the means of specifying the appropriate set of cycles
for which AlGaN is significant compared to the GaN layers.
1. Display the signal for Al in the active display tile.
2. Either using the table or the mouse (see below), select ranges of cycles
within the Matrix Index column of the table on the Calibration property
page.
262
3. Press the Define Interface button. Only those cycles selected in the
table will be assigned the VAMAS block reference Al[1].
Selecting Ranges of Cycles on the Calibration Property Page

Selecting rows within the Matrix Index table is achieved using the table
together with the Shift and Control Keys. Alternatively, the selection can be
defined using the active tile and the mouse. When the Shift Key is held down
and the left mouse button is used to drag over the display, the set of cycles
corresponding to those lying between the vertical cursors will be selected in
the Matrix Index table.
263
The use of the cursor and Shift key aids the identification of layered
structures viewed via a profile signal. Once a set of layers are so indicated,
the assignment is made by pressing the Define Matrix or Define Interface
button, as appropriate.
Surface Data and Background Signal

Since SIMS signal intensity depends on the matrix material, adventitious
carbon or other surface contaminants may result in signal from the surface
deviating from the bulk behaviour. It is therefore sometime appropriate to
exclude surface acquisition cycles from the RSF determination. Further a bulk
material may also cause a residual signal for the implant and therefore
removal of a background count rate is also appropriate. To aid the
specification of these two limitations when calculating RSF values, two
regions must me defined for each VAMAS block before an RSF can be
computed.
Defining the Surface and Background Regions:
1. Display any number of VAMAS blocks in the active display tile.
2. Press the Define Surf/BG button.
Two regions will appear on each profile; the left most region indicates the
peak and should be adjusted to start just after cycles associated with any
surface spike. The second right-most region defines the background to the
tail of an implant. Both regions can be adjusted using the Quantification
Parameters dialog window when viewing the Regions property page. The left
mouse button may be used to drag the start and end position of these
regions whenever the Region property page is active. Adjustment under
mouse control is available when grey vertical lines at either end of the
regions are displayed which appear when the Region property page is top-
most on the dialog window.
264
Three Ways to Calculate RSF Values from Standard Samples

Once the matrix and regions have been defined, the RSF can be computed by
the appropriate method:
Either: enter the Implant dose in Atoms/cm2 and the measured crater
depth in nanometres then press the Compute Sputter Rate button
before pressing the Compute RSF button. Pressing these buttons will
result in the corresponding values appearing in the boxes below the
buttons.
Alternatively, if a bulk doped standard is in use, tick the box labelled
Use Bulk Doped and enter the known atom density into the above
data input field. When a bulk doped standard is used to compute the
RSF, both the implant and matrix require regions.
The third method for computing the RSF is via a known implant depth
and atom density. The button to the right of the Depth field, namely,
results in a dialog window in which a depth and/or a
peak intensity can be entered. The position of the implant is defined
using the Matrix Index table by making a single selection in that table.
The appropriate cycle can be identified by left-clicking on the peak in
the left-hand pane active tile. The Matrix Index table scrolls to show
the cycle corresponding to the mouse selection and the table entry is
265
therefore offered for selection prior to invoking the Define Depth by

Cycle dialog window. If the correct depth and corresponding atoms per
cm3 are entered, the Calc RSF tick box is ticked and the OK button is
pressed, the RSF, Depth and Sputter Rate fields will be updated.
Adding RSF and Sputter Rates to Profile Data

Once an RSF is computed and the appropriate Sputter Rate entered for an
implant in a given matrix, the profile can be update with these values: select
a cycle from the Matrix Index table with the appropriate matrix entry and
press either the button or the button.
Each cycle within the profile with the same entry as the selected matrix index
will be updated with both the Sputter Rate and the RSF. If the material is a
multilayer structure the procedure should be repeated for each layer, where
the RSF and Sputter Rates are first determined from a standard profile. An
RSF/Sputter Rate pair can be extracted from another profile by first
displaying the profile, making a selection in the Matrix Index table and
pressing the button. The RSF/Sputter Rate from the indicated
matrix index will be entered into the fields on the dialog window, thus
allowing the unknown to be subsequently displayed and these restored
values from the standard used to update the unknown profile. Note, the
Dose and depth for single matrix material are computed when the button
Apply to Selected Matrix is pressed.
Applying Calibration Parameters to One or More Profiles

Once RSF and Sputter Rates have been assigned to each depth profile, the
data are calibrated by pressing the Calibrate Depth Profile button. If multiple
profiles are prepared and overlaid in the active tile, pressing the Calibrate All
Profiles button results in each profile, so selected, being calibrated and
266
entered into a single experiment frame. The depth scale units must be
selected prior to calibration using the tick box Use Nanometres.
Note: If normalization to the matrix is not requires, it is necessary to compute
the RSF with the same selection of the Normalize tick box.
Depth Profile Statistics: Areal Density and Decay Length

Areal Density and Decay Length are computed as part of the Depth Profile
Statistics. The procedure for calculating these statistics requires a pair of
cursors to be defined on the displayed profile in the active tile. The aim is to
mark the region over which the profile peak appears. To mark the cursors on
the profile: hold the Shift Key down and drag a box starting from the left of
the peak and ending at the right-hand end with the mouse positioned at the
intensity of the background. On pressing the Profile Statistics button a dialog
window appears showing the current text in the VAMAS block comment plus
a set of lines offering the new calculated profile statistics. If it is desired to
include these new lines in the VAMAS block comment, then the OK button
should be pressed, otherwise the Cancel button will exit without altering the
VAMAS block comment. Note, the text in the VAMAS block comment can be
edited within this window leaving only the information so required.
267
Maintaining Standards Library Files

Once standards have been prepared and RSF/Sputter Rates computed, these
depth profiles can be moved to other files containing profiles from standards.
The toolbar buttons allow VAMAS blocks to be copied into an

existing file and also delete from a file. If a number of standard material
profiles are located in a single file, the button offers a means of

searching the strings within a VAMAS block comment and those matched are
both selected in the right-hand pane of the experiment frame and are also
displayed in the scrolled list of display tiles. VAMAS block comments can be
edited using the toolbar button.
Step-by-Step Description of Quantification for a Multi-Layer

Sample
In this example, the desired result is to plot atomic density verses depth for
Mg implanted in Gallium. To achieve this end and owing to the layered
structure, four masses were monitored, where two labelled 69Ga and Al
define the layer structure while the trace labelled Ga2 represents a constant
matrix signal, to which the Mg signal is normalized.
268
Step 1: Define the Matrix

Display the matrix VAMAS block, namely, Ga2 in the activetTile. The block id
plus the VAMAS Block index for the trace will appear on the Calibration
property page of the Dynamic SIMS dialog window.
269
Select all the cycles under the Matrix Index column in the table on the
Calibration property page and press the Define Matrix button; the selected
entries under the Matrix Index column will change to Ga2[2], thereby
showing the matrix is defined.
Step 2: Define the Layer Structure

The structure of the material is GaN : AlGaN : GaN (Dr Shadi Shahedipour,
University of Albany, New York) therefore the matrix definition alone is not
sufficient to specify the cycles for which different sputter rates and RSF must
be assigned. Thus a sample such as this one requires the definition of
quantification information using the interface column within the table on the
Calibration property page. The AlGaN layer is characterized by the trace
labelled Al. To define a layer within the profile, the signal Al is used to select
the set of cycles recorded between the two interfaces.
Before using the mouse to indicate the interfaces, ensure there are no
selected cycles in the table on the Calibration property page. Clicking on any
column away from the Matrix Index column will de-select all cycles. Note,
repeated use of the mouse will add to the current selection, allowing
complex multilayer materials to be specified. Mark the AlGaN layer by
holding the Shift-Key down and then dragging a box from the left to the right
270
of the AlGaN peak. The result of such an action is shown in above. All the
cycles within the table on the Calibration property page between the vertical
cursors shown above are selected by the mouse action and so pressing the
Define Interface button on the same property page will cause the Interface
column in the table to be updated.
Step 3: Enter RSF and Sputter Rate Values

In this example the RSF and Sputter Rate for the two layers are assumed to
be known. All that is required is to add sputter rates and RSF for each of the
three layers; the values are entered on the Calibration property page. The
required information for quantification are two RSF and SR pairs, which must
be entered correspondingly for the GaN and AlGaN layers. Since the matrix
does not define the layer structure, the assignments are made by using the
Apply RSF/SR to Interface button. After displaying the Mg trace in the active
tile the RSF and sputter rate for each layer can be entered in turn. Since the
Interface column was initially all assigned 69Ga[0], the layer assignment
based on the Al signal only altered the range of cycles specified by the
vertical cursors. As a result the GaN layers are identified by the Interface
entries 69Ga[0]. Thus, both the GaN layers are assigned RSF and sputter rates
by selecting one cycle for which the interface column contains 69Ga[0],
entering the appropriate RSF/SR and pressing the Apply RSF/SR to Interface
271
button. Each cycle previously designated as part of the 69G [0] layer will
receive the RSF/SR pair.
Similarly, the AlGaN RSF/SR values are entered in the text-fields, one cycle
with an Interface column of Al[1] selected and the Apply RSF/SR to Interface
button pressed a second time. Again, each cycle designated as Interface Al[1]
will receive the RSF/SR pair.
Step 4: Calibrate Mg Profile

Calibration is performed by displaying the Mg profile in the active tile and
pressing the Calibrate Depth Profile button.
272
In this example, the only mass for which RSF/SR pairs are entered is Mg. The
SR are automatically assigned to all masses, however the RSF values for
masses other than Mg remain set equal to unity. A consequence of leaving an
RSF equal to unity is that on Calibration to atomic density and depth, masses
for which the RSF is equal to unity will be scaled to the atomic density range
of any properly calibrated masses. This allows an overlay with respect to the
calibrated traces, without requiring the RSF for all masses to be assigned
prior to calibration. Counts per second traces are available in the calibrated
experiment frame as the second corresponding variable (Ctrl PageUp/Crtl
Page Down).
273
An Example of Computing an RSF using Dose and Implant Peak

Depth
A profile was obtained from GaN undoped epi growth ion implanted with
24
Mg at a dose of 1.0e15 atoms per cm2. The depth at the peak of the Mg
counts is 77 nm. Computation of an appropriate RSF is performed as follows:
Step 1: Define the Matrix

Display the Ga2 matrix profile in the Active Tile, press the header button
labeled Matrix Index in the table to select all cycles and press the Define
Matrix push button on the Calibration property page. The table on the same
property page will update to show that the Matrix index for each cycle is now
assigned to the Ga2 profile.
Step 2: Define the Surface Layers and also the Background for the Mg
Profile
Display the Mg profile in the active tile and press the button labeled Define
Surf/BG. Two regions are created on the Mg profile. The left-most end of the
left-most region defines the surface layers, while the background to the right-
most of the two regions estimates the background to the Mg signal.
274
Step 3: Define the Depth Scale

In this example, the depth scale is defined to be 77nm at the maximum signal
for the Mg profile. Using the left-mouse button, click on the profile to
indicate the position of the Mg maximum values. The table entries on the
Calibration property page will scroll so that the cycle corresponding to the
position of the vertical cursor, which is located at the top of the visible
portion of the list. Select the entry at the top of the visible portion and press
the button next to the Depth (nm): label. A dialog window appears in which
the selected cycle index in already entered and a text-field for the Depth
(nm) corresponding to the indicated cycle can be input.
On pressing the OK button, the Calibration property page is updated with the
depth computed from the Define Depth by Cycle dialog window values.
Step 4: Enter the Dose and Compute the RSF

Enter the dose in atoms per cm2 on the Calibration property page and press
the button labelled Compute RSF. If the elemental RSF is required, the tick-
box just above the Compute RSF button should be ticked.
Step 5: Calibrate the Mg Profile

Once the RSF is computed and the sputter rate updated, the values for each
cycle corresponding to the Mg profile (currently displayed in the active tile)
must be updated. In this example, the assignment for the matrix is sufficient
to target the cycles for which RSF and sputter rates must be applied. Simply
select any cycle using the Matrix Index column in the table and press the
Apply RSF/SR to Matrix button. Since all the cycles are defined to have the
same matrix, the table for the Mg profile will contain values for the RSF and
sputter rate throughout. To calibrate the profile, press the button labelled
Calibrate Profile.
275
Note that the Profile Statistics button has been used to create a VAMAS
block comment showing the Areal Density and Decay Length for the Mg
profile. Also note how the profiles for which no RSF is specified are scaled to
allow their visualization within the same scale as the calibrated Mg profile.
Computing RSFs where the Matrix Signal is Measured following

the Completion of the Implant Profile
Cameca dynamic SIMS instruments permit experiments in which only the
implant is profiled. The inclusion of the matrix intensity in the computed RSF
is achieved by measuring the matrix signal after the implant signal attenuates
276
to background levels. The assumption is therefore that the matrix count rate
is constant during the acquisition of the dopant profile. While in principle the
Cameca files contain the experimental parameters for the profile, there are
occasions where the matrix reference signal must be inspected and manually
entered. To calculate the RSF for a standard material based on an implant
profile only, the following features are employed.
The VAMAS file for a single boron implant in silicon consists of a single
VAMAS block.
Following the measurement of the boron profile, the Cameca monitors the
matrix signal, and records the counts per second for the matrix in the data
file. It should be noted that the crater depth measured following such an
experiment includes the depth etched during the matrix measurement which
occurs after the boron profile is completed.
Calculation of the RSf for 11B implanted in silicon is computed identically to
previous examples with the exception that the user inputs the matrix signal
in counts per second via the Ref Signal button on the Calibration property
page. The VAMAS block containing the boron profile is updated with the
intensity of the matrix signal via the Reference Signal dialog window invoked
by the Ref Signal button.
277
Computing the RSF is performed as follows:

1. Enter the crater depth (770 nm) and press the Compute Sputter Rate
button.
2. Enter the dose (5x1014 atoms per cm2).
3. Check that the reference signal is correctly assigned and enter the
correct value by pressing the Ref Signal button.
4. Press the Compute RSF button.
Gathering Profile Data for Display and Calibration

Purposes
Profile data typically is stored as individual VAMAS files. There are however
reasons why merging these files into a single experiment frame is desirable.
For example, data can only be overlaid for display purposes for data located
in the same experiment frame. A further reason for moving profiles into a
single experiment frame is that Calibration of a dynamic SIMS profile is
performed on the Calibration property page and the button for calibrating
multiple profiles only acts on data within a given experiment frame. Copying
profiles into a single experiment frame permits many profiles to be calibrated
in one action.
By way of example, consider merging two VAMAS files containing profile data
for which a display of the data in overlay format is required.
1. Open each of the two data files in CasaXPS.
2. Using the Window menu, tile the two experiment frames so that both
right-hand panes are visible such that the VAMAS blocks are easily
selected.
278
3. Create a new experiment frame and press the Copy/Paste VAMAS

blocks toolbar button.
4. Check that the VAMAS blocks listed on the Copy Selection dialog
window match those selected in the two files and press the OK button.
279
The selected VAMAS blocks now appear in the new experiment frame. Note
that the selected VAMAS blocks are transferred to the experiment frame with
focus. In the event that the experiment frame with focus already contains
VAMAS blocks the selected VAMAS blocks are appended to the existing
blocks. The target experiment frame for this example was initially empty
therefore only the selected blocks appear in the experiment frame.
5. Save the new experiment frame to disk.
After preparing the profiles with appropriate RSFs and sputter rates the
entire set of profiles is calibrated by overlaying the implant VAMAS blocks in
the active tile and pressing the Calibration All Profile button.
280
A new experiment frame appears contain the quantified profiles.
281
XPS Instrument Transmission

Correction
Electron Spectroscopy
X-rays illuminate an area of a sample causing electrons to be ejected with a
range of energies and directions. The electron optics, possibly a combination
of electrostatic and/or magnetic lens units, collects a proportion of these
emitted electrons. Not all electrons emitted from the sample are transferred
through the apertures and focused onto the analyser entrance slit.
Electrostatic fields within the concentric hemispherical analyser (CHA or HSA)
are established to only allow electrons of a given energy, the so called Pass
Energy (PE), to arrive at the detector slits and onto the detectors. The
efficiency with which electrons are collected as counts at the detector varies
as a function of the kinetic energy
imparted to the electrons by the
photoionisation process. Therefore,
knowledge of these transmission
characteristics is fundamental to
proper quantification of XPS data.
A hemispherical analyser and transfer
lenses are typically operated in the two
most common modes, namely, Fixed
Analyser Transmission (FAT), also
known as Constant Analyser Energy (CAE), or Fix Retard Ratio (FRR) also
known as Constant Retard Ratio (CRR). In FAT mode, the pass energy of the
analyser is held at a constant value and it is entirely the job of the transfer
lens system to retard the given kinetic energy channel to the range accepted
by the analyser. Most XPS spectra are acquired using FAT. The alternative
mode, FRR, scans the lens system but also adjusts the analyser pass energy to
ŵĂŝŶƚĂŝŶ Ă ĐŽŶƐƚĂŶƚ ǀĂůƵĞ ĨŽƌ ƚŚĞ ƋƵĂŶƚŝƚǇ ͞ŝŶŝƚŝĂů ĞůĞĐƚƌŽŶ ĞŶĞƌŐǇ͟ ͬ
͞ĂŶĂůǇƐĞƌW͘͟dŚŝƐŵŽĚĞŝƐƚǇƉŝĐĂůůǇƵƐĞĚĨŽƌƵŐĞƌƐƉĞĐƚƌĂƐŝŶĐĞƚŚĞĞŶĞƌŐǇ
interval accepted by the detection system (i.e. resolution) increases with
kinetic energy and recovers weak peaks at high kinetic energies while
282
restricting the intense low energy background that could damage the
detection system.
Electrons of a specific initial kinetic energy are measured by setting voltages
for the lens system that both focus onto the entrance slit the electrons of the
required initial energy and retards their velocity so the kinetic energy after
passing through the transfer lenses matches the pass energy of the
hemispherical analyser. To record a spectrum over a range of initial excitation
energies it is necessary to scan the voltages applied to these transfer lenses;
the prescription for a lens voltage is known as a lens function. Each operating
mode for an instrument requires a lens function for each lens and these lens
functions are typically stored in some configuration file used by the
acquisition system. The efficiency with which electrons are sampled by a
spectrometer is very dependent on these lens functions and without properly
tuned lens functions the performance of an instrument can be severely
impaired. Even with a well-tuned system the collection efficiency varies
across the many operating modes and it is necessary to characterize an
instrument using a corresponding transmission function for each of the lens
modes, energy resolutions, aperture settings and spot-sizes of the x-ray
source.
Transmission correction is central to quantitative XPS. Without proper
transmission correction, a comparison of results measured from the same
sample using different operating modes for an instrument would show
significant variations in atomic concentrations. Thus, following any changes
to the lens functions, aperture positions and even changes due to detector
aging require the calibration of the intensity scale, which involves computing
the transmission functions for any operating mode used in practice.
Quantification of Spectra using Transmission Correction

A transmission function, when available, is included with the spectral data in
a VAMAS block as a second corresponding variable. Transmission functions
are either:
1. Added to the data by the acquisition system e.g. SpecsLab 2 and Kratos
Vision 2 VAMAS files.
2. Added to the data when converted through CasaXPS to the ISO 14976
format e.g. PHI Multipak, Thermo Avantage ASCII, Kratos KAL ASCII and
SPECSLAB 1.
283
3. If the transmission function is available in certain formats, added to the

data using options on the Intensity Calib property page on the
Spectrum Processing dialog window e.g. instruments calibrated with
the NPL intensity calibration system.
Provided a transmission function is included in the ISO 14976 (VAMAS) file,

CasaXPS by default applies the transmission correction to the intensity values
used to compute the atomic concentration displayed in quantification
reports. Spectra displayed in the active tile appear as uncorrected intensities;
however quantification tables, either displayed as annotation over the
spectra or in the form of a text report include the transmission correction as
part of the atomic concentration calculation. The percentage atomic
concentration Xi is computed using the formula:
where the adjusted intensities Ai are determined from the measured

intensity Ii, the transmission function T evaluated for electrons of recorded
energy E, the relative sensitivity factor Ri for the transition i and the escape
depth compensation exponent n:
The column headed Area in the quantification report:
284
is corrected for transmission and escape depth, but does not include the
relative sensitivity factor. If desired, all terms used in the quantification
calculation, such as raw intensity in CPSeV or the transmission function value
at the peak maximum, can be output in a Standard Report on the Report
Spec property page. Obtaining the itemized quantification report involves
using the configuration files described elsewhere.
Library %At
Block Id Name Position Raw Area Transmission
RSF Conc
Cu/Au Au 4d 334.6 1.29E+06 18.9596 701.806 39.31
Cu/Au Cu 2p 931.6 1.85E+06 24.5703 841.33 60.69
The quantification table is computed using the parameters defined in the

table of quantification regions.
285
These parameters include the background type, the range of energies over
which the background subtracted data is integrated to obtain the value for Ii
in counts per second eV and the relative sensitivity factor (RSF). In principle,
the RSF corrects the raw intensity for sample and transition specific intensity
variations, in contrast to the transmission and escape depth correction terms,
which are in general fixed for all samples and correct the measured intensity
for instrumental influences. These instrumental corrections are controlled by
the settings in the Intensity Calibration section on the Regions property page.
By way of example, the escape depth correction is assigned a value of -0.7, a

value commonly used by SSI instruments. Note the exponent is given a
negative value. This is because CasaXPS, for historical reasons, makes the
correction to the intensity using the expression I*En rather than I/En. The fact
that the transmission correction is active is indicated by the tick box labelled
Automatic. For the data in the current example, a transmission function is
included in the VAMAS block, therefore by default the Automatic tick box is
ticked when the file is loaded into CasaXPS. The consequence of the
Automatic tick box being ticked is the area reported in the quantification
report over the spectrum is adjusted for transmission and escape depth.
A transmission function is added to a spectrum by including an additional
corresponding variable in the VAMAS block containing the data. As stated
above, the ticked state of the Automatic tick-box is an indicator that a
transmission function is present in a data block. Visual inspection of the
transmission function can be made by holding the Control key down and
pressing the Page Up keyboard key. To return to the spectrum, use the
Control key together with the Page Down key to step back to the display of
the corresponding variable containing the spectral data. The transmission for
the Au/Cu spectrum when displayed in the active tile using the Control +
Page Up keyboard keys is as follows:
286
The correction to the intensity for transmission and escape depth is made by
evaluating the functions at the position of the peak maximum before any
energy calibration is performed to the peak positions.
Practical Solutions to Transmission Correction

Certain file formats include as part of the description of the data a
transmission function. For example, the PHI Multipak files include a
correction function of the form:
The PHI transmission function represents a scaling function for moving

between pass energies within a lens mode. The objective of such a correction
is to allow the comparison of intensities measured using different pass
energies, where the parameters a and b are determined in a relative sense
from a set of calibration spectra. PHI and Thermo offer intensity calibration
functional forms, both of which are included in the VAMAS block created by
CasaXPS when the data is converted from either file format to the ISO format
used in CasaXPS. Kratos and SPECS SpecsLab2 also offer relative transmission
correction; these transmission functions are written into the VAMAS files
exported from the Vision Processing and SpecsLab2 systems.
287
The National Physical Laboratory UK offers an alternative solution to

calibrating an XPS instrument. A transmission function is calculated using
spectral background information, such that the intensity calibrated spectra
can be quantified using a theoretically determined RSF library, namely
Schofield cross-sections. The Scofield cross-sections may need modifying for
angular distribution variations resulting from an angle between the x-ray
source and the axis of the analyser differing from the magic angle (54o 44͛). If
calibrated using the NPL system, the possibility of all laboratories, regardless
of instrument, using the same basic RSF library producing equivalent
quantifications is conceivable. The transmission curve presented above was
created using the NPL calibration software for a Kratos Axis Ultra at
University of Manchester.
Adding a Transmission Function to SPECS SpecsLab1

Data
A transmission function file can be added to the CasaXPS file system which is
read each time a SpecsLab1 data file is converted to the ISO 14976 format.
288
The ASCII file CasaXPS.trf, located in the same directory as the CasaXPS.exe
executable file, is searched each time a SpecsLab1 exp file is converted
through CasaXPS. The CasaXPS.trf file contains a set of transmission function
definitions identified by the string used to specify an aperture. The exact set
of parameters and functional form is determined from the entry in the
CasaXPS.trf file. The following table shows an entry from an exp file where
the aperture and the set of aperture strings are marked to illustrate the
strings of importance to the transmission function file.
EnergyAnalyser: phoiboss
{
ea_mode = esca_c_ep;
ea_serial = 0;
ea_vers = 0;
ea_const = 50;
ea_ampl_fact = 0;
ea_particle_polarity = -1;
ea_detector_U = 2300;
ea_conversion_U = 0;
ea_aperture = 3;
ea_is_small_spot = 0;
ea_nchannels = 5;
ea_addinfo = "";
ea_apertures = "[Area 4x10:7x20:40mm][Area 3x10:7x20:40mm][Area
2x6:7x20:30mm][Area 1x3:7x20:30mm][Area 0.5dia:7dia:20mm][Area
0.1dia:1dia:10mm][UPS:7dia:20mm][ISS:7x20:50mm][AES:7x20:50mm][BAES:7x20:50mm]";
}
289
A file which included the aperture list and aperture parameter (an index
starting at zero) as specified in the table would cause the second function
defining in the table below to be loaded into a newly converted ISO file.
[Area 3.0:MM:7x20:40mm PE* ?]

functiontype5 2 -0.5
[Area 1x3:7x20:30mm PE* ?]

functiontype6
Response Function Parameter a0 +2.260820
Response Function Parameter a1 -19.874343
Response Function Parameter a4 -27.316750
Response Function Parameter b1 -8.950412
Response Function Parameter b2 +20.326906
Response Function Parameter b3 +15.764882
Response Function Parameter b4 -10.226651
An entry in the CasaXPS.trf file consists of a header string delimited by a pair

of square brackets, followed on the next line by a function-type string, which
determines the meaning of the parameters that follow. The two entries are
examples of functiontype5 the standard SPECS prescription for the analyser
transmission: T(E)=aE-b and funtctiontype6 the set of parameters determined
by the NPL calibration system:
T(E)=(a0+a1y+a2y2+a3y3+a4y4)/(1+b1y+b2y2+b3y3+b4y4)
where y = (E-1000.0)/1000.0. The parameter list below the string

functiontype6 can be copied and pasted into the CasaXPS.trf file directly from
the Q.vms file output from the NPL calibration system. The functiontype6 NPL
transmission function format appears in CasaXPS version 2.3.13 and above.
Adding a Transmission Function to Data Blocks

Adding or replacing a transmission function to a set of VAMAS blocks is
achieved via the Intensity Calib property page on the Spectrum Processing
dialog window.
290
Three options are available for modifying an existing transmission function:

1. The Add Transmission Function from File button is pressed. A file
containing the transmission function information is read and added to
any blocks selected in the right-hand pane of the experiment frame.
2. PHI coefficients are entered in the text-fields adjacent to the Change
Phi TF button. Again, the transmission function is added to the
selected blocks in the right-hand pane of the experiment frame.
3. Similar to option 2 but the Thermo VG coefficients are used to
compute the transmission function rather than the PHI.
Add Transmission Function from File

There are three file formats accepted by the Add Transmission Function from
File button:
1. A simple ASCII format where the first line is an integer format number,
which must be 1. The next line is a positive integer specifying the
number of energy, transmission function pairs which follow, one pair
per line. The values for the energy and transmission function values
must be separated by a space or a TAB.
2. A Q.vms file generated by the NPL Calibration system. The Q.vms file
provides a VAMAS description of the transmission function, followed
by the parameters and the results of the calibration process. When the
291
Q.vms file is read into CasaXPS, it is the parameter set which is used to
compute the transmission function, the VAMAS fields are ignored.
3. A CasaXPS.trf formatted file. When a SpecsLab1 exp is converted, two
strings are added to the VAMAS block comment tagged with the prefix
͞dZ&^dZ/E'ϭ͗͟ĂŶĚ͞dZ&^dZ/E'Ϯ͗͘͟dŚĞƐĞƐƚƌŝŶŐƐĂƌĞƚĂŬĞŶĨƌŽŵƚŚĞ
aperture list in the exp file and are used to extract a transmission
function, on a block by block basis, from the CasaXPS.trf formatted file.
Transmission functions read from file are added to all data blocks selected in
the right-hand pane of the experiment frame prior to pressing the button.
Relative Sensitivity Factors and Instrument

Geometry
In an ideal world, if a sample were analysed using a range of different
instruments, the results presented as atomic concentrations would be
entirely consistent regardless of type of XPS instrument used to make the
measurements. The consistency of these measurements represents the
precision with which these measurements can be made by the
instrumentation in use. The accuracy obtained for the atomic concentrations
is determined by the relative sensitivity factors (RSFs) used to scale the
measured intensities for the different elements. Again, in an ideal world, a
single set of RSFs offering the relative intensity of photoelectric lines for each
nl-electron observed for a given x-ray anode would exist and could be applied
to all samples. The goal of absolute accuracy based on a single set of RSFs for
all samples is unattainable for many reasons; however the concept of relative
accuracy is the accepted goal for many analysts using XPS. That is, assuming
all instruments were calibrated for intensity variations due to transmission,
then one would like to use a common RSF library to ensure the same
quantification is reported irrespective of which instrument made the analysis.
Scofield (J. Electron Spectrosc. Relat. Phenom. 8, 129 (1976)) compiled a set
of photo-ionisation cross-sections for aluminium and magnesium x-ray
sources. In principle these describe the relative intensities for the various
photoelectric lines observed in the energy spectra. In practice, the principle
of this statement is only true provided the x-ray source and energy analyser
are at the, so called, magic angle of 54o 44͛. For all other angles between
these two mechanical components the relative sensitivity for the different
transitions changes due to the angular distribution of photoelectrons ionized
292
by un-polarized light impinging on an nl-shell electron. The equation

describing the angular distribution is given by (Reilman et al, J. Electron
Spectrosc. Relat. Phenom. 8, 389 (1976)):
where ɸ is the photoelectron energy, ʍnl;ɸͿ is the cross-section for photo-

ionizing an nl ĞůĞĐƚƌŽŶ;^ĐŽĨŝĞůĚͿ͕ɽŝƐƚŚĞĂŶŐůĞďĞƚǁĞĞŶƚŚĞƉŚŽƚŽŶĂŶĚƚŚĞ
photoelectron direction:
and .
ɴnl;ɸͿ, the asymmetry parameter, like ʍnl;ɸͿ also depends on the wave
function. The complexity of the intensity variation with transition is removed
for instruments such that P2(cos ɽ)=0 Žƌ ɽ = 54o 44͛, for which the term
involving ɴnl;ɸͿdrops out of the equation above. For instruments where the
ĂŶŐůĞ ɽ differs from the magic angle, the Scofield cross-sections must be
corrected to account for the non-zero term involving ɴnl;ɸͿ. Sadly, most
instruments to date do not use the magic angle between the analyser and x-
ray source and therefore tables of asymmetry parameters are required to
modify the RSF tables containing values appropriate for the magic angle
configuration.
293
PHI Multipak Data

Data from a range of PHI instruments saved in PHI Multipak file formats may
be converted to VAMAS format through CasaXPS.
PHI 5000 Versa Probe

To convert a file in Multipak format:
1. Select the Convert option on the File menu or via the top toolbar of
CasaXPS.
2. Move to the directory containing the Multipak file.
3. Selecting the file into the File name text-field on the File dialog
window.
4. Press the Open button on the File dialog window.

294
The data within the Multipak file is converted from the binary format to the
ISO 14976 VAMAS ASCII file format. Each acquisition region in the original
Multipak format appears as a VAMAS block in the right-hand pane of the
CasaXPS experiment frame.
The data from the first row of VAMAS blocks are displayed in the left-hand
pane using a scrolled list of display tiles.
Multipak saves data in files with a range of file extensions depending on the
nature of the data within the file. A set of spectra measured at the same
position on a sample under the same conditions is saved in a file with
extension spe as illustrated above. The following illustrates other file formats
used by Multipak.
295
Angle Resolver XPS (ARXPS) are saved with file extension ang:
The tilt angle used to acquire the data appears as an experimental variable in
the VAMAS file. Each row of VAMAS blocks represents data acquired using
the same angle.
Sputter depth profile data are assigned the file extension pro:
Image files are saved with various file extensions: map, sem, sxi:
296
Image files with the file extension map include an image per detector
available to the instrument. Processing of these energy-separated images can
offer a significant improvement in the image information.
Quantification of PHI Spectra

The key steps to quantification of PHI data in CasaXPS are:
1. Converting the MultiPak binary files through CasaXPS to obtain VAMAS
files which include the PHI transmission function correction.
2. Prepare an element library in CasaXPS format containing the PHI
sensitivity factors.
3. Configure CasaXPS to make the angular distribution adjustments to the
PHI sensitivity factors appropriate for the PHI instrument from which
the data derives.
The Convert to VAMAS option in CasaXPS accepts files of many formats and
converts the data into an equivalent ISO 14976 (VAMAS) format. In the case
of PHI data, MultiPak binary files include information about the transmission
function and also the angle between the analyser and the x-ray source. When
the spectra are converted through CasaXPS, these data are also included in
the VAMAS file and provide the means for adjusting the intensities of the
spectra for transmission variation with kinetic energy of the recorded
electrons, and the adjustments to the library sensitivity factors for the
instrument geometry used to acquire the spectra.
While the transmission function is automatically applied by CasaXPS to the
intensities used to calculate atomic concentrations, the sensitivity factors in
the PHI library must be entered into a CasaXPS formatted library file; these
sensitivity factors are corrected by CasaXPS at time of use. Provided the
appropriate configuration entries are included in the
CasaXPS.DEF/ParameterFile.txt file, whenever a sensitivity factor is extracted
297
from the element library, the appropriate adjustments for angular

distribution are applied to the library sensitivity factor. The approach of
maintaining a library of magic angle sensitivity factors which are corrected for
a given piece of data is consistent with the approach adopted by PHI. By
adjusting the sensitivity factors for the given data, data from different PHI
instruments can be accommodated using the same library. The PHI Quantum
series of instruments, including the Versa Probe, use an angle of 45° between
the analyser and the x-ray source, while a 5600 instrument uses an angle of
90°; data from both instrument geometries are quantified under the PHI
regime using the same element library adjusted for angular distribution.
Creating a PHI Library

The CasaXPS library file is a simple ASCII file containing TAB separated rows of
information for each transition. The default CasaXPS library contains Scofield
cross-sections, which appear, if loaded into a spreadsheet program such as
Excel, in the ninth column.
The simplest strategy for populating an element library with sensitivity

factors is to load the CasaXPS library file into Excel and set all the values in
the RSF column to zero before entering those sensitivity factors most
commonly used. Once a basic library file is established, in the future, each
time a new sensitivity factor is requires, the value can be entered using the
mechanism in CasaXPS for adding or changing an entry in the CasaXPS library.
Editing an Element Library Entry

The default CasaXPS library is loaded at the time CasaXPS execution begins.
As CasaXPS starts, the CasaXPS.exe executable file loads a file named
CasaXPS.lib located in the same directory as the CasaXPS.exe file.
The format for a library file includes a standard set of ten fields per transition.
298
1. Element
2. Transition
3. Label/Name
4. Mass (Daltons)
5. Energy Type (BE or KE)
6. Energy (eV)
7. F.W.H.M.
8. Line shape (e.g. GL(30))
9. Relative Sensitivity Factor
10.Excitation source string
The photoionisation cross-section for electrons ejected by scattering with
incident photons is dependent on the energy of the photon source. For this
reason the element library may contain the same transition repeated for all
possible x-ray gun anode materials. The two most commonly used anode
materials are magnesium and aluminium, however silver and chromium are
also used on occasion. The default CasaXPS library contains entries for Mg
and Al anodes specified via field 10, namely, Excitation Source string, where
different Scofield cross-sections for photon energies 1253.6 eV and 1486.6 eV
are entered in field 9, Relative Sensitivity Factor (RSF). The library mechanism
is designed to display the appropriate transitions and RSFs for the data in the
active tile.
The excitation source string in the element library is used to select the
appropriate transitions for the data displayed in the active tile. By default,
when a Multipak file is converted through CasaXPS the VAMAS block field for
the source label is assigned the string either Mg or Al, based on the
information in the original file. A spectrum converted from a Multipak file
specifying an aluminium anode, when displayed in the active tile, causes the
Element Table property page of the Element Library dialog window to offer
those library entries with excitation source Al. Auger transitions with
excitation source label ANY will also appear in the element table.
299
Modifying an entry displayed in the element table is achieved by placing the

cursor over the name field and right-clicking the mouse.
The dialog window invoked by the mouse action allows entries to be

modified or a new library entry created depending on the button pressed to
exit the dialog window.
300
The modified element library is written back to file only on exit from the
CasaXPS main program. A file dialog offers a means of specifying the
directory and name for the modified element library file. To make the
modified element library file the default element library, move the file to the
directory containing the CasaXPS executable and ensure the base name of
the library file matches the base name of the executable.
When preparing entries in the CasaXPS element library suitable for use with
PHI data, it is important to ensure the name field in the CasaXPS library entry
matches the region string used by the PHI acquisition software. The RSF
entered into a newly created region or component will be extracted from the
element library by matching the element/transition fields in the VAMAS
blocks to the name-fields in the element library. For modern version of the
PHI acquisition system, the acquisition names for the spectral regions
typically match the default names used in the CasaXPS library. Older PHI
systems tend to use a naming convention not so informative and so it may be
necessary to adjust these strings to conform to the name-strings in the
CasaXPS library or adjust the name strings in the CasaXPS library to match
those used in the PHI data files.
301
Examples of the older PHI conventions are Fe1 meaning Fe 2p and Cr1
meaning Cr 2p. An alternative to manually adjusting these strings to match
the element library name-fields is to configure an automatic assignment for
the data converted from the PHI data files.
Automatic Adjustment of Acquisition Names

Version 2.3.15 of CasaXPS includes an option for automatically adjusting the
names used by older version of the PHI acquisition system to match the
name-fields in the element library. A configuration line added to the
CasaXPS.DEF/ParameterFile.txt file instructs CasaXPS to examine the
acquisition parameters associated with the regions defined in the Multipak
files to determine the appropriate element library entry for the data.
To enable this option, the text string:

update phi element transition fields
must be added to the ParameterFile.txt file in the CasaXPS.DEF directory.
Once CasaXPS is restarted, each PHI Multipak file when converted through
CasaXPS will be labelled using the most appropriate element library entry for
the data.
The configuration option transforms the original names for the acquisition
regions:
302
To element/transitions strings matching the element library entries:
Creating Quantification Regions

A typical multiplex Multipak data file includes a survey spectrum together
with a set of high resolution narrow scan spectra. To create a quantification
table from these data, the simplest approach is based on quantification
regions. Quantification regions specify how to compute the intensity for a
particular transition and therefore form the basis for measuring the
elemental composition of a sample. Often the energy resolution used to
measure a survey spectrum is sufficient for obtaining an elemental
quantification for a sample.
Quantification for a polymer sample measured on a PHI 5000 Versa Probe
will be used to illustrate the features in CasaXPS.
Quantification of a Survey Spectrum

The polymer sample is a fluorinated HDPE material. The survey spectrum
shows significant evidence of fluorine, oxygen and carbon. The bare
minimum requirement in terms of relative sensitivity factors is therefore RSFs
for the transitions F 1s, O 1s and C 1s. The default CasaXPS library can be
made to form the skeleton for a library suitable for Multipak data by
changing the RSFs previously assigned Scofield cross-sections to have zero
values. The transitions for which RSFs are required are added to the skeletal
file using a spreadsheet program and saved as a TAB delimited ASCII file.
303
When loaded into CasaXPS, the new library file offers only three non-zero
RSFs for F 1s, O 1s and C 1s.
Creating quantification regions is performed explicitly using the

Quantification Parameters dialog window, however for survey spectra the
Element Table property page or the Periodic Table property page on the
Element library dialog window provide a quick means of creating regions
directly from the element library information. To create a set of regions:
1. Using the Element Table or the Periodic Table property pages, place
peak markers on the survey spectrum.
304
2. Press the Create Regions button.
Quantification regions created using the Element Library dialog window

ensure RSFs are extracted from the element library appropriate for the name
used to label the region. The user is still responsible for ensuring the named
region spans the appropriate peak or, in the case of the double pairs, peaks.
A simple mechanism based on the zoom-list maintained for the active tile
permits the region limits and suitability of the background for the peaks
selected for quantification to be assessed and adjusted. After the regions are
created, pressing the Reset toolbar button loads the set of regions onto the
zoom-list.
Subsequently, each time the zoom out toolbar button is pressed, the display
in the active tile offers a close-up view of a region.
If the Region property page is top-most on the Quantification Parameters

dialog window, adjustments to the region limits can be made using the
mouse or directly via the text-fields on the property page.
305
Use of the Create Regions buttons on the Element Library dialog window also
causes the creation of an annotation table.
The format and position of the annotation table are altered via the
Annotation dialog window.
Quantification of the survey spectrum requires the correct sensitivity factors

corresponding to the transmission correction for the instrument recording
the spectrum. Multipak data files include the information about the
transmission function in the header section of the file. When the Multipak
file is converted by CasaXPS, the transmission function is added to the
VAMAS file and automatically included in the calculation of the atomic
concentrations reported for the spectrum. The transmission function is
added as a second corresponding variable to each VAMAS block; the first
corresponding variable contains the spectral data. To view the transmission
function the keyboard key sequence Control + Page Up steps upwards
through the corresponding variables, while Control + Page Down causes the
reversal of the Control + Page Up step.
306
While the Multipak data include these transmission functions, PHI

recommend good practice dictates that quantification is performed based on
data recorded using the same lens mode and pass energy; a recommendation
endorsed here and appropriate for all XPS data regardless of instrument
origin.
Quantification based on Narrow Scan Spectra

Multiplex data appear in an experiment frame as a row of VAMAS blocks.
The simplest way to add regions to a set of multiplex data is to select the
VAMAS blocks corresponding to the narrow scan spectra in the right-hand
pane of the experiment frame before pressing the Add Regions toolbar
button.
307
One region is added to each narrow scan spectrum for which the VAMAS
block is selected in the right-hand pane. The RSF and name for each region
created by this means is determined from the element/transition VAMAS
block fields. It is therefore important to ensure these are correctly assigned
prior to pressing the toolbar button.
Quantification reports generated from the Report Spec property page of the
Quantification Parameters dialog window require the VAMAS blocks to
appear in the same row in the right-hand pane.
A texted based report is generated from the Standard Report section on the
Report Spec property page. The contents of the report are determined by a
configuration file and appear within CasaXPS as an additional window. To
generate a report from a set of VAMAS blocks:
1. Select a row of VAMAS blocks for which quantification regions are
defined.
2. For a report generated from quantification regions, press the button
labelled Regions in the Standard Report section of the Report Spec
property page.
State of the selection before pressing the Regions button:
308
State of the display after pressing the Regions button:
The quantification report contains the results for only three of the six spectra
selected in the right-hand pane even though all the spectra have regions
defined. The reason only three of the intended six regions are included in the
report is because the skeletal element library only contained non-zero RSFs
for O 1s, C 1s and F 1s. The N 1s, S 2p and Si 2p RSFs are all zero in the library;
therefore the quantification regions for these data were assigned zero RSFs
too. Any region with a zero RSF is excluded from any quantification report. To
remedy the problem, the regions must be updated with the appropriate non-
zero RSFs.
309
The N 1s data can be updated using the value for the RSF listed in the PHI
Manual; however the S 2p and Si 2p regions differ from the manual entries
for the RSFs due to angular distribution intensity variations; since the 45°
angle between the x-ray source and the analyser of the Versa Probe used to
collect the spectra differs from the magic angle, the RSF value becomes
instrument dependent and must be calculated from the library RSF. To make
the modification to the PHI Manual RSF value for a p-orbital, the manual RSF
should be entered into the CasaXPS library and the quantification region RSF
updated in turn from the value stored in the CasaXPS element library.
To enable the modification of RSFs based on the instrument geometry, a
configuration entry must be added to the file named ParameterFile.txt
located in the CasaXPS.DEF directory. The string:
correct for angular distribution
must be entered onto a separate line of the configuration file:
The element library entries for N 1s, S 2p and Si 2p can be updated as

described above. Once entered into the CasaXPS library, the values for the
RSF fields in the quantification regions are also updated using the name field
for the region. Enter the name used in the element library for the name field
in the region and add the # character as a prefix.
After the Enter keyboard key is pressed, the name field is entered into the
region without the # character and the RSF is updated with the corrected RSF
value.
310
The retrieved RSF is modified appropriately from the value for the S 2p
entered into the CasaXPS library:
After repeating the process of updating the RSFs for each of the Si 2p and N
1s regions, the quantification report generated using identical steps to those
above produces the report containing results for all six spectra.
311
Quantification of Thermo Scientific Data

The last ten years have seen the XPS technique develop from a technique
used predominantly by experts of XPS to a tool used by application oriented
scientists. The emergence of instruments such as the Thermo Scientific K-
Alpha shows that there is a place for an instrument with a high performance
to cost ratio and lower cost of ownership. Instruments with these
characteristics offer a route for the XPS technique into application areas
previous limited by the constraints of expensive high performance
technology. There will always be a place for high performance systems run by
experts, but these new low cost XPS systems can only be good for surface
science.
The data from the Thermo Scientific K-Alpha is supported in version 2.3.15 of
CasaXPS, where a number of enhancements are included to streamline the
conversion and processing of the new ASCII files. The ASCII files exported
from the K-Alpha include a new flag to indicate whether or not the intensities
are corrected for transmission. Version 2.3.15 of CasaXPS detects the new
flag and converts the ASCII file to the ISO 14796 format using the counts-per-
bin computed from the transmission corrected data. The necessity of
returning the data to counts-per-bin lies in the assumption that the noise in
the data is governed by Poisson statistics, which is required when measuring
the goodness-of-fit and when performing Monte Carlo error analysis on peak
models. The ISO file written by CasaXPS includes both the counts-per-bin and
also the transmission functions from the ASCII file, therefore quantification of
312
the spectra in CasaXPS proceeds exactly the same way as for other data
acquired using the Thermo Avantage data system.
An attractive feature of the K-Alpha is the possibility of combining a new
resource with existing high performance instruments, either in-house or
available from external laboratories. To accommodate the use of more than
one instrument, data converted from a K-Alpha have a unique source label
assigned to each VAMAS block and hence entries specific to the K-Alpha can
be added to the CasaXPS element library. This feature permits the default
CasaXPS library to offer the appropriate RSFs for data from different
instruments.
A new toolbar button provides a further means of creating

quantification regions for a set of VAMAS blocks based on the
element/transition fields in the VAMAS blocks. When converted from the
Avantage ASCII files, the spectra are assigned the element/transition fields
based on the name assigned to the data. For example, a carbon 1s transition
ŵŝŐŚƚ ĂƉƉĞĂƌ ŝŶ ƚŚĞ ǀĂŶƚĂŐĞ ĚĂƚĂ ĨŝůĞǁŝƚŚ ƚŚĞ ŶĂŵĞ ͞ ϭƐ ^ĐĂŶ͟ Žƌ ͞ ϭƐ
^ŶĂƉ͕͟ ĚĞƉĞŶĚŝŶŐ ŽŶ ƚŚĞ ĂĐƋƵŝƐŝƚŝŽŶ ŵŽĚĞ͘ KŶ ĐŽŶǀĞƌƐŝŽŶ ƚŽ /^K ĨŽƌŵĂƚ
through CasaXPS, these strings are used to eǆƚƌĂĐƚ ƚŚĞ ĞůĞŵĞŶƚ ͟͞ ĂŶĚ
ƚƌĂŶƐŝƚŝŽŶ ͞ϭƐ͘͟ƌŵĞĚ ǁŝƚŚ ƚŚĞƐĞ ƐƚƌŝŶŐƐ͕ ƚŚĞ ŶĞǁ ƚŽŽůďĂƌ ďƵƚƚŽŶ ŝĚĞŶƚŝĨŝĞƐ
the entry corresponding to the photoelectric line in the element library and
uses the element library information to create regions for each selected
VAMAS block correctly assigned in terms of element/transition.
Converting Avantage Data

Data from the K-Alpha are exported from the Avantage system as ASCII files.
These ASCII files can be converted as follows.
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Thermo Scientific Avantage Files

The Avantage binary files must be converted via an Avantage utility program
(DataSpace_BatchDump.exe) to ASCII equivalent files. These ASCII files are
created with the file extension .avg and can be converted to ISO 14976
(VAMAS) format using the Convert to VAMAS dialog window available from
the File menu or the top toolbar of CasaXPS:
1. Using the Avantage utility program DataSpace_BatchDump.exe,
convert all the .vgd binary files for an experiment to .avg ASCII files.
2. Select the Convert to VAMAS dialog window in CasaXPS either using
the toolbar button or via the Convert menu item on the File menu.
3. Move to the directory containing the .avg ASCII files; the

DataSpace_BatchDump.exe program offers the user the choice of
where the ASCII files should be created.
4. Enter a name for the new VAMAS file using the file extension .avg and
press the Open button. For example, if you wish to call your new file
sample001.vms, then you should enter sample001.avg into the file
name field on the Convert to VAMAS file dialog window. Each .avg file
found in the current directory will be read and entered into the new
VAMAS file named sample001.vms.
A directory of ASCII files is converted to a single VAMAS file as follows.

Enter the name for the new VAMAS file followed by the file extension avg:
314
A new ISO file named steel_highres.vms will be created from the set of avg
files in the current directory Scan_0.
Note how the base-name for the ISO file is used together with the .avg
conversion switch to instruct CasaXPS to read the set of .avg files in the
directory and converted all the files in the directory to a single ISO format
file. Each avg file in the directory contains two spectra per file, before and
after etching the sample surface, hence the two rows of VAMAS blocks in the
VAMAS file.
Merging Sets of Experiments

The acquisition regions for each experiment are exported into separate ASCII
files with the .avg extension, thus an experiment is typically recorded, once
exported, as a set of ASCII files in a directory. If an experiment is one in a
sequence of experiments, all of which might reasonably be processed as a
315
unit, then a further import option allows a set of such data directories to be
converted to a single ISO 14976 VAMAS file.
Given a set of directories each containing exported Avantage data, a new
VAMAS file is created by moving to the directory using the Convert to VAMAS
File Dialog containing these data sub-directories and entering the new
filename with an extension of .mvg.
A VAMAS file with the extension .vms is created at the level of the directory
containing the data sub-directories. The .avg files found in the sub-directories
are converted and entered into the new VAMAS file with the experimental
variable set to a Data Set index number. The index assigned to the
experimental variable is dependent on the order of the sub-directories when
read. In addition to the Data Set index, the rows are also assigned labels
based on the names given to the sub-directories, which can be view using the
Edit Mode toolbar button.
Quantification
The principal features used to quantify data from the K-Alpha can be
discussed using survey spectra:
316
Element Library Excitation Source String

The following is a survey spectrum measured using a K-Alpha instrument,
exported to ASCII format and converted to ISO format using CasaXPS.
The header above the spectrum includes the source string assigned by
CasaXPS for the aluminium anode, namely, KA1486. The significance of the
unique source string assignment for the K-Alpha data is that the KA1486
string allows a set of element library entries to be prepared for use with the
K-Alpha data. When a spectrum is displayed in the active tile in CasaXPS, the
element library entries visible on the Element Table property page are
selected based on a match between the source string stored in the VAMAS
block for the spectral data and the Excitation Source string located in the
element library file.
317
The element library file may contain entries for use with different
instruments, and provided the excitation source strings are different for the
different instruments, only those entries appropriate for a given instrument
will be displayed in the element table. Thus, if a laboratory owned a PHI
Quantum 2000, say, and also a Thermo Scientific K-Alpha, the element library
entries for the PHI instrument could be populated with the excitation source
strings Al while the K-Alpha will be assigned KA1486. On loading data from
the PHI Quantum, CasaXPS will use and display only the entries with
excitation source Al, while similarly K-Alpha data in CasaXPS cause the display
of the K-Alpha sensitivity factors on the Element Table property page.
Transmission Function
The transmission function for the K-Alpha is included in the ISO file created
by CasaXPS. To view the transmission function in CasaXPS, hold down the
Control key on the keyboard and press the PageUp or PageDown keys to
switch between a display of the transmission curve or return to the spectral
data. The transmission function for the survey spectrum above, when viewed
in CasaXPS, appears as follows.
The quantification table annotating the spectrum computes the atomic

concentrations using the raw area for each peak assigned a quantification
region. CasaXPS divides the raw background subtracted area by the
transmission function and the relative sensitivity factor, then applies the
energy dependent correction calculated from the energy exponent (entered
on the Regions property page) to the adjusted peak intensity.
318
The default energy dependent exponent for the K-Alpha used with the
Scofield cross-sections is -0.6; the value used for the K-Alpha data is
configured in the CasaXPS.DEF/ParameterFile.txt file, so other values for the
exponent are possible. An example of the ParameterFile.txt file illustrates the
configuration entry used to define the default value for the energy exponent.
The highlighted line specifies the energy exponent added to the data when
converted from the Avantage ASCII files.
Preparing an Element Library for use with the K-Alpha

The Avantage element library information is stored in a Microsoft Access
database file. The libraries supplied with Avantage are covered by the
319
Avantage software license agreement and the original libraries or any

converted formats must not be distributed. However, Thermo have made
the library format available to enable individual users to obtain consistent
results between Avantage and CasaXPS.
Using Microsoft Access to open the .mdb file, select the Peaks table and copy
the table into Excel. The Peaks table, viewed in Excel, can then be written to a
Tab Delimited ASCII file for use in CasaXPS. Once the Tab Delimited ASCII file
is available, the sensitivity factors from the Avantage system are loaded into
CasaXPS using the Input File property page on the Element Library dialog
window:
1. hƐĞ ƚŚĞ ƌŽǁƐĞ ͙ ďƵƚƚŽŶ ŽŶ ƚŚĞ /ŶƉƵƚ &ŝůĞ ƉƌŽƉĞƌƚǇ ƉĂŐĞ ƚŽ ŝĚĞŶƚŝĨǇ
the Peaks table file written from Excel.
2. Select the VG Av. Wagner or VG Av Scofield radio buttons on the same

property page, depending of the sensitivity factors desired.
3. Press the Load button to replace the current CasaXPS library with the
values from the Avantage Peak table file.
4. Exit CasaXPS, at which point CasaXPS will prompt for the filename used
to save the modified element library. Save the element library to a new
filename, e.g. CasaXPS_AvScofield.lib.
5. Open the newly created library file in Excel and globally change the
source label strings as follows. The newly created file will contain rows
for each transition in the original Peaks table file which will include
entries for both Al and Mg anodes. Globally change the Al anode string
to KA1486 and the Mg anode string to KA1253.
320
6. If another instrument using different RSFs is also in use, in Excel, open

the current CasaXPS.lib file located in the CasaXPS directory containing
the CasaXPS.exe executable file. Copy the entries from the newly
created and source label adjusted CasaXPS formatted file
corresponding to the K-Alpha library into the Excel file containing the
current CasaXPS.lib file. The resulting spreadsheet should contain all
the existing enters followed by all the entries from the Avantage file in
CasaXPS format. After saving the resulting table of CasaXPS formatted
entries to file, the combined file will need to replace the default
CasaXPS library file called CasaXPS.lib in the directory containing the
CasaXPS.exe executable file.
Once the new element library is prepared and in the correct location,
CasaXPS will need to be restarted and data from each type of instrument
examined. Load a spectrum from each of the instruments involved, open the
Element Table property page and click on the tile displaying the spectra.
Ensure the Ex. Source column displays the correct anode label for the data
being viewed and also the RSF column is appropriate for the spectrum in the
active tile.
Given an appropriate element library prepared as described above, data from
either instrument will be quantified in exactly the same way. Each time a
region or component is created using the element library, the appropriate
RSF for the data will be retrieved from the combined element library.
321
Quantification of JEOL XPS Spectra from SpecSurf

The quantification procedure used by the JEOL SpecSurf software involves
modifying the Scofield cross-sections to account for both an energy
dependency and also angular distribution corrections. However, to reproduce
the quantification tables in CasaXPS produced by the JEOL SpecSurf software,
it is sufficient to use an energy exponent equal to -0.2, entered on the
Regions property page, and the unaltered Scofield cross-sections for the RSF
values.
While the reported RSFs will not match in absolute terms, the relative RSFs
are the same between the two systems and therefore the quantification
tables will be identical (assuming the same calculated peak areas and
positions for the peaks).
Although the infrastructure for adjusting the RSFs for angular distribution is
ŝŶƉůĂĐĞĨŽƌƚŚĞ:K>ƐŽĨƚǁĂƌĞ͕ƚŚĞĐƵƌƌĞŶƚ:K>ƐǇƐƚĞŵƐĞƚƐƚŚĞĂƐǇŵŵĞƚƌǇɴ
parameter to unity and therefore the angular distribution function returns
the same value for all transitions, hence the Scofield cross-sections are all
scaled by the same factor. The only significant adjustment to the
quantification values derive from the energy dependency. The actual
modifications to the Scofield cross-sections applied by the JEOL system can
be fully reproduced in CasaXPS version 2.3.15, where a set of configuration
parameters defined in the ParameterFile.txt file in the CasaXPS.DEF directory
control the calculated RSFs. When initialised using an angle of 56° between
322
the x-ray source and the analyser, and an energy exponent of -0.2,
numerically equivalent RSF values are reproduced in CasaXPS. The following
table are results from CasaXPS.
Name Position Library RSF Total RSF Raw Area %At Conc
C 1s 284.7 1.01548 4.19415 6367.69 58.1
N 1s 401.2 1.82786 7.39709 78.6979 0.4
O 1s 532.4 2.97535 11.7345 2740.05 8.9
F 1s 688.6 4.49857 17.1189 3212.83 7.2
Si 2p 100.4 0.829645 3.5258 2337.71 25.4
The RSFs should be compared to the RSFs reported for the same data by the
JEOL software:
The small differences between the total RSFs reported by CasaXPS and those
from the JEOL software are due to different peak positions between the two
systems, probably due to slight differences in the background definition.
In order to obtain quantification tables from CasaXPS consistent with the
JEOL software, it is necessary to add lines to the ParameterFile.txt file in the
CasaXPS.DEF directory as follows:
The JEOL element library includes the asymmetry parameters and therefore,
should these be implemented in future releases of the JEOL software the line
ŝŶ ƚŚĞ WĂƌĂŵĞƚĞƌ&ŝůĞ͘ƚǆƚ ĨŝůĞ ͞ũĞŽů ĂŶŐƵůĂƌ ĚŝƐƚƌŝďƵƚŝŽŶ͟ ǁŽƵůĚ ŶĞĞĚ ƚŽ ďĞ
ĐŚĂŶŐĞĚƚŽ͞ĐŽƌƌĞĐƚĨŽƌĂŶŐƵůĂƌĚŝƐƚƌŝďƵƚŝŽŶ͘͟tŝƚŚƚŚŝƐĂĚũƵƐƚŵĞŶƚ͕ĂƐĂyW^
would extract RSFs from a Scofield library to include the full angular
distribution correction.
323
The theory behind the use of angular distribution correction is discussed in

detail elsewhere in the CasaXPS manual. An outline of the procedure will be
given below.
The default CasaXPS library is populated with Scofield cross-sections. These

Scofield cross-sections are computed from Hartree-Slater wave-functions and
therefore are appropriate for an XPS instrument designed with the, so called,
magic angle between the x-ray source and the analyser axis. Given the angle
between the x-ray source and the analyser, a correction can be made to
these magic angle RSFs appropriate for the given instrument. The
configuration file method for specifying the require angle for the JEOL
instrument, which is 56° is shown below.
Each time one or more files are opened in CasaXPS for which the angle has
yet to be set, a dialog window prompts the user for the missing angle and
offers the configured angle as the default.
Once a file is updated with an entry in the VAMAS file comment of the form
͞^ŽƵƌĐĞŶĂůǇƐĞƌŶŐůĞ͗ϱϲ͘ϬϬϬϬϬϬĚ͕͟ƚŚĞƐŽƵƌĐĞƚŽĂŶĂůǇƐĞƌĂŶŐůĞŝƐĚĞĨŝŶĞĚ
ĨŽƌ ƚŚĂƚ ĨŝůĞ͘ tŚĞŶ ĐŽƵƉůĞĚ ǁŝƚŚ ƚŚĞ ĐŽŶĨŝŐƵƌĂƚŝŽŶ ĞŶƚƌǇ͕ ͞ũĞŽů ĂŶŐƵůĂƌ
distrŝďƵƚŝŽŶ͕͟ ƚŚĞ ŵĂŐŝĐ ĂŶŐůĞ ^ĐŽĨŝĞůĚ ĐƌŽƐƐ-sections from the element
library will be adjusted each time an RSF is extracted from the element library
for use with a Region or Component. The Total RSF in the table above
calculated by CasaXPS is computed from the RSF in the Region or Component
multiplied by the energy dependence defined by the value in the text-field on
the Regions property page.
324
XPS Spectra
The XPS technique is used to investigate the chemistry at the surface of a
sample.
Figure 47: Schematic of an XPS instrument.
The basic mechanism behind an XPS instrument is illustrated in Figure 47.

Photons of a specific energy are used to excite the electronic states of atoms
below the surface of the sample. Electrons ejected from the surface are
energy filtered via a hemispherical analyser (HSA) before the intensity for a
defined energy is recorded by a detector. Since core level electrons in solid-
state atoms are quantized, the resulting energy spectra exhibit resonance
peaks characteristic of the electronic structure for atoms at the sample
surface. While the x-rays may penetrate deep into the sample, the escape
depth of the ejected electrons is limited. That is, for energies around 1400
eV, ejected electrons from depths greater than 10nm have a low probability
of leaving the surface without undergoing an energy loss event, and
therefore contribute to the background signal rather than well defined
primary photoelectric peaks.
In principle, the energies of the photoelectric lines are well defined in terms
of the binding energy of the electronic states of atoms. Further, the chemical
environment of the atoms at the surface result in well defined energy shifts
to the peak energies. In the case of conducting samples, for which the
detected electron energies can be referenced to the Fermi energy of the
spectrometer, an absolute energy scale can be established, thus aiding the
325
identification of species. However, for non-conducting samples the problem

of energy calibration is significant. Electrons leaving the sample surface cause
a potential difference to exist between the sample and the spectrometer
resulting in a retarding field acting on the electrons escaping the surface.
Without redress, the consequence can be peaks shifted in energy by as much
as 150 eV. Charge compensation designed to replace the electrons emitted
from the sample is used to reduce the influence of sample charging on
insulating materials, but nevertheless identification of chemical state based
on peak positions requires careful analysis.
XPS is a quantitative technique in the sense that the number of electrons

recorded for a given transition is proportional to the number of atoms at the
surface. In practice, however, to produce accurate atomic concentrations
from XPS spectra is not straight forward. The precision of the intensities
measured using XPS is not in doubt; that is intensities measured from similar
samples are repeatable to good precision. What may be doubtful are results
reporting to be atomic concentrations for the elements at the surface. An
accuracy of 10% is typically quoted for routinely performed XPS atomic
concentrations. For specific carefully performed and characterised
measurements better accuracy is possible, but for quantification based on
standard relative sensitivity factors, precision is achieved not accuracy. Since
many problems involve monitoring changes in samples, the precision of XPS
makes the technique very powerful.
The first issue involved with quantifying XPS spectra is identifying those
electrons belonging to a given transition. The standard approach is to define
an approximation to the background signal. The background in XPS is non-
trivial in nature and results from all those electrons with initial energy greater
than the measurement energy for which scattering events cause energy
losses prior to emission from the sample. The zero-loss electrons constituting
the photoelectric peak are considered to be the signal above the background
approximation. A variety of background algorithms are used to measure the
peak area; none of the practical algorithms are correct and therefore
represent a source for uncertainty when computing the peak area. Peak
areas computed from the background subtracted data form the basis for
most elemental quantification results from XPS.
326
Figure 48: An example of a typical XPS survey spectrum taken from a compound sample.
The data in Figure 48 illustrates an XPS spectrum measured from a typical

sample encountered in practice. The inset tile within Figure 48 shows the
range of energies associated with the C 1s and K 2p photoelectric lines. Since
these two transitions include multiple overlapping peaks, there is a need to
apportion the electrons to the C 1s or the K 2p transitions using a synthetic
peak model fitted to the data. The degree of correlation between the peaks
in the model influences the precision and therefore the accuracy of the peak
area computation.
Relative sensitivity factors of photoelectric peaks are often tabulated and

used routinely to scale the measured intensities as part of the atomic
concentration calculation. These RSF tables can only be accurate for
homogenous materials. If the sample varies in composition with depth, then
the kinetic energy of the photoelectric line alters the depth from which
electrons are sampled. It is not uncommon to see evidence of an element in
the sample by considering a transition at high kinetic energy, but find little
evidence for the presence of the same element when a lower kinetic energy
transition is considered. Transitions of this nature might be Fe 2p compared
to Fe 3p both visible in Figure 48, where the relative intensity of these peaks
will depend on the depth of the iron with respect to the surface. Sample
roughness and angle of the sample to the analyser also changes the relative
327
intensity of in-homogenous samples, thus sample preparation and mounting

can influence quantification values.
Figure 49: Germanium Oxide relative intensity to elemental germanium measured using
photoelectrons with kinetic energy in the range 262 eV to 272 eV.
Figure 50: Germanium Oxide relative intensity to elemental germanium measured using
photoelectrons with kinetic energy in the range 1452 eV to 1460 eV.
The chemical shifts seen in XPS data are a valuable source of information
about the sample. The spectra in Figure 49 and Figure 50 illustrate the
separation of elemental and oxide peaks of germanium due to chemical
state. Both spectra were acquired from the same sample under the same
conditions with the exception that the ejected electrons for the Ge 3d peaks
are about 1200 eV more energetic that the Ge 2p electrons. The
328
consequence of choosing to quantify based on one of these transitions is that

the proportion of oxide to elemental germanium differs significantly. The
oxide represents an over layer covering of the elemental germanium and
therefore the low energy photoelectrons from the Ge 2p line are attenuated
resulting in a shallower sampling depth compared to the more energetic Ge
3d electrons. Hence the volume sampled by the Ge 2p transition favours the
oxide signal, while the greater depth from which Ge 3d electrons can emerge
without energy loss favours the elemental germanium. While these variations
may seem a problem, such changes in the spectra are also a source for
information about the sample.
Tilting the sample with respect to the axis of the analyser results in changing
the sampling depth for a given transition and therefore data collected at
different angles vary due to the differing composition with depth. Figure 51 is
a sequence of Si 2p spectra measured from the same silicon sample at
different angles. The angles associated with the spectra are with respect to
the axis of the analyser and the sample surface. Data measured at 30°
favours the top most oxide layers; while at 90° the elemental substrate
becomes dominant in the spectrum.
Figure 51: Angle resolved Si 2p spectra showing the changes to the spectra resulting from
tilting the sample with respect to the analyser axis.
329
Other Peaks in XPS Spectra
Not all peaks in XPS data are due to the ejection of an electron by a direct
interaction with the incident photon. The most notable are the Auger peaks,
which are explained in terms of the decay of a more energetic electron to fill
the vacant hole created by the x-ray photon, combined with the emission of
an electron with an energy characteristic of the difference between the
states involved in the process. The spectrum in Figure 48 includes a sequence
of peaks labelled O KLL. These peaks represent the energy of the electrons
ejected from the atoms due to the filling of the O 1s state (K shell) by an
electron from the L shell coupled with the ejection of an electron from an L
shell.
Unlike the photoelectric peaks, the kinetic energy of the Auger lines is
independent of the photon energy for the x-ray source. Since the kinetic
energy of the photoelectrons are given in terms of: the photon energy h ,
the binding energy for the ejected electron E be and a work function by the
relationship E ke h Ebe , altering the photon energy by changing the x-
ray anode material causes the Auger lines and the photoelectric lines to
move in energy relative to one another.
Figure 52: Elemental Silicon loss peaks and also x-ray satellite peak.
Less prominent than Auger lines are x-ray satellite peaks. Data acquired using
a non-monochromatic x-ray source create satellite peaks offset from the
330
primary spectral lines by the difference in energy between the resonances in

the x-ray spectrum of the anode material used in the x-ray gun and also in
proportion to the peaks in the x-ray spectrum for the anode material. Figure
52 indicates an example of a satellite peak to the primary Si 2p peak due to
the use of a magnesium anode in the x-ray source. Note that Auger line
energies are independent of the photon energy and therefore do not have
satellite peaks.
A further source for peaks in the background signal is due to resonant

scattering of electrons by the surface materials. Plasmon peaks for elemental
silicon are also labelled on Figure 52. The sharpness of these plasmon peaks
in Figure 52 is due to the nature of the material through which the
photoelectrons must pass. For silicon dioxide, the loss structures are much
broader and follow the trend of a typical XPS background signal. The sharp
loss structures in Figure 52 are characteristic of pure metallic-like materials.
Basic Quantification of XPS Spectra

XPS counts electrons ejected from a sample surface when irradiated by x-
rays. A spectrum representing the number of electrons recorded at a
sequence of energies includes both a contribution from a background signal
and also resonance peaks characteristic of the bound states of the electrons
in the surface atoms. The resonance peaks above the background are the
significant features in an XPS spectrum shown in Figure 53.
Figure 53: XPS and Auger peaks appear above a background of scattered
electrons.
331
XPS spectra are, for the most part, quantified in terms of peak intensities and
peak positions. The peak intensities measure how much of a material is at the
surface, while the peak positions indicate the elemental and chemical
composition. Other values, such as the full width at half maximum (FWHM)
are useful indicators of chemical state changes and physical influences. That
is, broadening of a peak may indicate: a change in the number of chemical
bonds contributing to a peak shape, a change in the sample condition (x-ray
damage) and/or differential charging of the surface (localised differences in
the charge-state of the surface).
Figure 54: Quantification regions
The underlying assumption when quantifying XPS spectra is that the number
of electrons recorded is proportional to the number of atoms in a given state.
The basic tool for measuring the number of electrons recorded for an atomic
state is the quantification region. Figure 54 illustrates a survey spectrum
where the surface is characterised using a quantification table based upon
values computed from regions. The primary objectives of the quantification
region are to define the range of energies over which the signal can be
attributed to the transition of interest and to specify the type of
approximation appropriate for the removal of background signal not
belonging to the peak.
332
Figure 55: O 1s Region
How to Compare Samples
A direct comparison of peak areas is not a recommended means of

comparing samples for the following reasons. An XPS spectrum is a
combination of the number of electrons leaving the sample surface and the
ability of the instrumentation to record these electrons; not all the electrons
emitted from the sample are recorded by the instrument. Further, the
efficiency with which emitted electrons are recorded depends on the kinetic
energy of the electrons, which in turn depends on the operating mode of the
instrument. As a result, the best way to compare XPS intensities is via, so
called, percentage atomic concentrations. The key feature of these
percentage atomic concentrations is the representation of the intensities as a
percentage, that is, the ratio of the intensity to the total intensity of electrons
in the measurement. Should the experimental conditions change in any way
between measurements, for example the x-ray gun power output, then peak
intensities would change in an absolute sense, but all else being equal, would
remain constant in relative terms.
Relative Intensity of Peaks in XPS
Each element has a range of electronic states open to excitation by the x-

rays. For an element such as silicon, both the Si 2s and Si 2p transitions are of
333
suitable intensity for use in quantification. The rule for selecting a transition
is to choose the transition for a given element for which the peak area, and
therefore in principle the RSF, is the largest, subject to the peak being free
from other interfering peaks.
Transitions from different electronic states from the same element vary in
peak area. Therefore, the peak areas calculated from the data must be scaled
to ensure the same quantity of silicon, say, is determined from either the Si
2s or the Si 2p transitions. More generally, the peak areas for transitions from
different elements must be scaled too. A set of relative sensitivity factors are
necessary for transitions within an element and also for all elements, where
the sensitivity factors are designed to scale the measured areas so that
meaningful atomic concentrations can be obtained, regardless of the peak
chosen.
Figure 56: Regions Property Page.
Quantification of the spectrum in Figure 54 requires the selection of one

transition per element. Figure 55 illustrates the area targeted by the region
defined for the O 1s transition; similar regions are defined for the C 1s, N 1s
and Si 2p transitions leading to the quantification table displayed over the
data in Figure 54. The Regions property page shown in Figure 56 provides the
basic mechanism for creating and updating the region parameters influencing
the computed peak area. Relative sensitivity factors are also entered on the
Regions property page. The computed intensities are adjusted for instrument
334
transmission and escape depth corrections, resulting in the displayed

quantification table in Figure 54.
Quantification regions are useful for isolated peaks. Unfortunately not all
samples will offer clearly resolved peaks. A typical example of interfering
peaks is any material containing both aluminium and copper. When using the
standard magnesium or aluminium x-ray anodes, the only aluminium
photoelectric peaks available for measuring the amount of aluminium in the
sample are Al 2s and Al 2p. Both aluminium peaks appear at almost the same
binding energy as the Cu 3s and Cu 3p transitions. Thus estimating the
intensity of the aluminium in a sample containing these elements requires a
means of modelling the data envelope resulting from the overlapping
transitions illustrated in Figure 57.
Figure 57: Aluminium and Copper both in evidence at the surface.
Overlapping Peaks
Techniques for modelling data envelopes not only apply to separating

elemental information, such as the copper and aluminium intensities in
Figure 57, but also apply to chemical state information about the aluminium
itself. Intensities for the aluminium oxide and metallic states in Figure 57 are
measured using synthetic line-shapes or components. An XPS spectrum
typically includes multiple transitions for each element; while useful to
identify the composition of the sample, the abundance of transitions
335
frequently leads to interference between peaks and therefore introduces the

need to construct peak models. Figure 58 illustrates a spectrum where a thin
layer of silver on silicon (University of Iowa, Jukna, Baltrusaitis and Virzonis,
2007, unpublished work) introduces an interference with the Si 2p transition
from the Ag 4s transition.
The subject of peak-fitting data is complex. A model is typically created from

a set of Gaussian/Lorentzian line-shapes. Without careful model construction
involving additional parameter constraints, the resulting fit, regardless of
how accurate a representation of the data, may be of no significance from a
physical perspective. The subject of peak fitting XPS spectra is dealt with in
detail elsewhere.
Peak models are created using the Components property page on the
Quantification Parameters dialog window shown in Figure 59. A range of line-
shapes are available for constructing the peak models including both
symmetric and asymmetric functional forms. The intensities modelled using
these synthetic line-shapes are scaled using RSFs and quantification using
both components and regions are offered on the Report Spec property page
of CasaXPS.
Figure 58: Elemental and oxide states of Silicon

336
Peak Positions
In principle, the peak positions in terms of binding energy provide

information about the chemical state for a material. The data in Figure 48
provides evidence for at least three chemical states of silicon. Possible
candidates for these silicon states might be SiO2, Si2O3, SiO, Si2O or Si,
however an assignment based purely on the measured binding energies for
the synthetic line-shapes relies on an accurate calibration for the energy
scale. Further, the ability to calibrate the energy scale is dependent on the
success of the charge compensation for the sample and the availability of a
peak at known binding energy to provide a reference for shifting the energy
scale.
Figure 59: Components property page on the Quantification Parameters dialog window.
Charge Compensation
The XPS technique relies on electrons leaving the sample. Unless these
emitted electrons are replaced, the sample will charge relative to the
instrument causing a retarding electric field at the sample surface. For
conducting samples electrically connected to the instrument, the charge
balance is easily restored; however, for insulating materials electrons must
be replaced via an external source. Insulating samples are normally
electrically isolated from the instrument and low energy electrons and/or
337
ions are introduced at the sample surface. The objective is to replace the
photoelectrons to provide a steady state electrical environment from which
the energy of the photoelectrons can be measured.
The data in Figure 60 shows spectra from PTFE (Teflon) acquired with and
without charge compensation. The C 1s peaks are shifted by 162 eV between
the two acquisition conditions, but even more importantly, the separation
between the C 1s and the F 1s peaks differ between the two spectra by 5 eV.
Without effective charge compensation, the measured energy for a
photoelectric line may change as a function of kinetic energy of the electrons.
Charge compensation does not necessarily mean neutralization of the sample

surface. The objective is to stabilize the sample surface to ensure the best
peak shape, whilst also ensuring peak separation between transitions is
independent of the energy at which the electrons are measured. Achieving a
correct binding energy for a known transition is not necessarily the best
indicator of good charge compensation. A properly charge compensated
experiment typically requires shifting in binding energy using the Calibration
property page, but the peak shapes are good and the relative peak positions
are stable.
Figure 60: Insulating sample before and after charge compensation.
338
A nominally conducting material may need to be treated as an insulating

sample. Oxide layers on metallic materials can transform a conducting
material into an insulated surface. For example, aluminium metal oxidizes
even in vacuum and a thin oxide layer behaves as an insulator.
Calibrating spectra in CasaXPS is performed using the Calibration property

page on the Spectrum Processing dialog window.
Depth Profiling using XPS
Figure 61: Segment of an XPS depth profile.
While XPS is a surface sensitive technique, a depth profile of the sample in

terms of XPS quantities can be obtained by combining a sequence of ion gun
etch cycles interleaved with XPS measurements from the current surface. An
ion gun is used to etch the material for a period of time before being turned
off whilst XPS spectra are acquired. Each ion gun etch cycle exposes a new
surface and the XPS spectra provide the means of analysing the composition
of these surfaces.
The set of XPS spectra corresponding to the oxygen 1s peaks from a depth
profile experiment depicted logically in Figure 61 are displayed in Figure 62.
The objective of these experiments is to plot the trend in the quantification
values as a function of etch-time.
339
Figure 62: The set of O 1s spectra measured during a depth profiling experiment.
The actual depth for each XPS analysis is dependent on the etch-rate of the
ion-gun, which in turn depends on the material being etched at any given
depth. For example, the data in Figure 62 derives from a multilayer sample
consisting of silicon oxide alternating with titanium oxide layers on top of a
silicon substrate. The rate at which the material is removed by the ion gun
may vary between the layers containing silicon oxide and those layers
containing titanium oxide, with a further possible variation in etch-rate once
the silicon substrate is encountered. The depth scale is therefore dependent
on characterizing the ion-gun however each XPS measurement is typical of
any other XPS measurement, with the understanding that the charge
compensation steady state may change between layers.
Figure 63: XPS Depth Profile of silicon oxide/titanium oxide multilayer sample profiled using
a Kratos Amicus XPS instrument.
340
Figure 64: Logical structure of the VAMAS blocks in an XPS depth profile.
The XPS depth profile in Figure 63 is computed from the VAMAS file data
logically ordered in CasaXPS as shown in Figure 64. The O 1s spectra
displayed in Figure 62 are highlighted in Figure 64. One point to notice about
the profile in Figure 63 is that the atomic concentration calculation for the O
1s trace is relatively flat for the silicon oxide and titanium oxide layers, in
contrast to the raw data in Figure 62, where the chemically shifted O 1s
peaks would appear to be more intense for the silicon oxide layers compared
to the titanium oxide layers. This observation is supported by the plot of
adjusted peak areas in Figure 65, where again the O 1s trace is far from flat.
The profile in Figure 63 is far more physically meaningful than the variations
displayed in Figure 65. Normalization of the XPS intensities to the total signal
measured on a layer by layer basis is important for understanding the
sample. This example is a good illustration of why XPS spectra should be
viewed in the context of the other elements measured from a surface.
The details of how to analyze a depth profile in CasaXPS are discussed at

length in The Casa Cookbook and other manual pages available from the Help
option on the Help menu.
341
Figure 65: Peak areas scaled by RSF used to compute the atomic
concentration plots in Figure 63.
342

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CasaXPS Manual 2.3.15 Rev 1.

0 Copyright © 2009 Casa Software Ltd

CasaXPS Manual 2.3.15

Element Library Format ............................................................................................... 100

Converting IonToF Spectra .................................................................................. 155

Profile Directory Toolbar Option ..................................................................... 159

The Element Library from a ToF Perspective ...............................................................166

Create a Total Ion Spectrum .............................................................................181

Spectra Generated from Profile Layers .............................................................189

Create a Profile from a Directory of Files ..........................................................189

Convert and Merge a Directory of XYT File .......................................................192

Image Depth Profile Data Analysis ...............................................................194

Dynamic SIMS .................................................................................................................. 240

Creating a PHI Library ...............................................................................................298

CasaXPS Main Window

The Main Window of CasaXPS is a multiple document interface capable of

Experiment frames may appear full sized.

Experiment frames may be tiled.

Or as icons within the CasaXPS Main Window.

Loading Data into CasaXPS

A file dialog window allows data to be selected from disk.

Displaying Data in CasaXPS

Selection of Data using the Mouse

Specifying the number of rows (or columns):

Zooming into Data

The zoom list is re-initialised by pressing the reset toolbar button:

Reset Zoom out

Loads regions Step to region

Return to the initial display state.

Adjustments to the energy interval accompanied by rescaling of the intensity

Drag zoom box over Zoom in

Energy interval shifted

The Processing History property page lists the processing currently

Basic Energy Calibration

Essentially, charge compensation is performed by specifying the location of a

determined. The calculated shift may be applied to one or more spectra as

Charge Compensation for a Set of High Resolution Spectra

Press the Apply to Selection button.

Creating Backgrounds and Regions

Region names are user-defined names used to reference the information

A Relative Sensitivity Factor or RSF for a peak identified by a region is

Two additional parameters influence the intensity of the background at the

Quantification of Survey Spectrum using Regions

To calibrate the energy scale for an individual spectrum:

Select the Spectrum processing dialog window

Select the Calibration property page

An annotation table offering a quantification table is added to the spectrum.

The quantification table may be repositioned on the data using the

With the Annotation History property page top-most on the Annotation

It is also advisable to check the quantification regions created automatically

Following an adjustment to the limits, the annotation table and Regions

Manual Creation of Regions

To create regions one at a time:

1. Invoke the Quantification Parameters dialog window and ensure the

Creating Peak Models

The Regions property page is used to define a background to the data

The intensity from a quantification region can be explicitly excluded from a

Components are created using the Element Table property page in an

While it would be possible at this stage in the peak modelling process to