Personalized medicine by a time-of-flight MS database approach Prescribed pharmaceutical drugs ar... more Personalized medicine by a time-of-flight MS database approach Prescribed pharmaceutical drugs are only effective in sub-cohorts of the general population, but not in all patients who are medicated. Current diagnostics fail to accurately predict the individuals who are going to benefit most from a specific agent, who would likely not see effects and who would be better treated by an different medicine. SNP genotyping is a promising tool towards personalized medicine, but it can only be used for general genetic predispositions for diseases nd drug efficacy. In order to pinpoint the current state of an individual, including metabolic absorption and turnover rates, mass spectrometry-based metabolomics can be used to discern metabolism before and after drug treatment. EDTA-blood plasma was used from patient cohorts in a variety of drug response phenotype studies for comprehensive metabolite extraction by cold protein precipitation at -20C and iPrOH/ACN/H2O (vol.ratio 30:1, mixture 5/2/2...
Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells c... more Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC) adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05). Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection.
Overview Purpose Published metabolomic studies so far have involved less than 200 individual samp... more Overview Purpose Published metabolomic studies so far have involved less than 200 individual samples. Such surveys are accomplished within a week without too much drift of instrument sensitivity or retention time shifts. We show how quality control charts and standard operating procedures maintain high data quality even in larger programs. Equally important are the detection, alignment and annotation of individual deconvoluted peaks for over 1,000 chromatograms. If each deconvoluted 'signal' is taken into consideration, lists of target peaks expand to thousands of entries. We here demonstrate how severe constraints on mass spectral purity, s/n ratios and detection frequency manage unbiased metabolomics data in large scale experiments . Methods A Leco corp. Pegasus III GC-TOF was equipped with a dual arm CTC robotic derivatization station and an ATAS automatic liner exchange and direct thermodesorption injection device. Quality control was achieved by seven standard operating...
SUMMARY: Metabolomic publications and databases use different database identifiers or even trivia... more SUMMARY: Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including
Metabolomics is the methodology that identifies and measures global pools of small molecules (of ... more Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and transcriptomics. This paper describes the analysis of Arabidopsis metabolomics data sets acquired by a consortium that includes five analytical laboratories, bioinformaticists, and biostatisticians, which aims to develop and validate metabolomics as a hypothesis-generating functional genomics tool. The consortium is de...
The metabolite profile changes induced by Fe deficiency in leaves and xylem sap of several Strate... more The metabolite profile changes induced by Fe deficiency in leaves and xylem sap of several Strategy I plant species have been characterized. We have confirmed that Fe deficiency causes consistent changes both in the xylem sap and leaf metabolite profiles. The main changes in the xylem sap metabolite profile in response to Fe deficiency include consistent decreases in amino acids, N-related metabolites and carbohydrates, and increases in TCA cycle metabolites. In tomato, Fe resupply causes a transitory flush of xylem sap carboxylates, but within 1 day the metabolite profile of the xylem sap from Fe-deficient plants becomes similar to that of Fe-sufficient controls. The main changes in the metabolite profile of leaf extracts in response to Fe deficiency include consistent increases in amino acids and N-related metabolites, carbohydrates and TCA cycle metabolites. In leaves, selected pairs of amino acids and TCA cycle metabolites show high correlations, with the sign depending of the F...
Saccharophagus degradans is a potent degrader of marine and plant cell wall polysaccharides. In p... more Saccharophagus degradans is a potent degrader of marine and plant cell wall polysaccharides. In particular, it is capable of degrading and metabolizing agarose that is the main component of marine red algae. To understand its degradation and metabolism of agarose along with the agarase expression profile, S. degradans was grown using different carbon sources including galactose, agarose, glucose and cellulose. The metabolite profiling was conducted by using GC-TOF MS and in-house programmed database, BinBase. When the metabolite profiles of cells on galactose and agarose were compared, principal component analysis of 133 identified metabolites revealed clear separations between the groups on galactose and agarose. S. degradans grown on agarose was found to use different carbon catabolic pathways from that grown on other carbon sources. The metabolite profile of cells grown using galactose had increased abundances of glycerol, glycerol derivatives and fatty acids. The use of polysaccharides such as agarose or cellulose led to the increased abundances of amino acids and intermediates of nucleotide biosynthesis.
Iron homeostasis is an important process for flower development and plant fertility. The role of ... more Iron homeostasis is an important process for flower development and plant fertility. The role of plastids in these processes has been shown to be essential. To document the relationships between plastid iron homeostasis and flower biology further, a global study (transcriptome, proteome, metabolome, and hormone analysis) was performed of Arabidopsis flowers from wild-type and triple atfer1-3-4 ferritin mutant plants grown under iron-sufficient or excess conditions. Some major modifications in specific functional categories were consistently observed at these three omic levels, although no significant overlaps of specific transcripts and proteins were detected. These modifications concerned redox reactions and oxidative stress, as well as amino acid and protein catabolism, this latter point being exemplified by an almost 10-fold increase in urea concentration of atfer1-3-4 flowers from plants grown under iron excess conditions. The mutant background caused alterations in Fe-haem redox proteins located in membranes and in hormone-responsive proteins. Specific effects of excess Fe in the mutant included further changes in these categories, supporting the idea that the mutant is facing a more intense Fe/redox stress than the wild type. The mutation and/or excess Fe had a strong impact at the membrane level, as denoted by the changes in the transporter and lipid metabolism categories. In spite of the large number of genes and proteins responsive to hormones found to be regulated in this study, changes in the hormonal balance were restricted to cytokinins, especially in the mutant plants grown under Fe excess conditions.
Personalized medicine by a time-of-flight MS database approach Prescribed pharmaceutical drugs ar... more Personalized medicine by a time-of-flight MS database approach Prescribed pharmaceutical drugs are only effective in sub-cohorts of the general population, but not in all patients who are medicated. Current diagnostics fail to accurately predict the individuals who are going to benefit most from a specific agent, who would likely not see effects and who would be better treated by an different medicine. SNP genotyping is a promising tool towards personalized medicine, but it can only be used for general genetic predispositions for diseases nd drug efficacy. In order to pinpoint the current state of an individual, including metabolic absorption and turnover rates, mass spectrometry-based metabolomics can be used to discern metabolism before and after drug treatment. EDTA-blood plasma was used from patient cohorts in a variety of drug response phenotype studies for comprehensive metabolite extraction by cold protein precipitation at -20C and iPrOH/ACN/H2O (vol.ratio 30:1, mixture 5/2/2...
Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells c... more Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC) adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05). Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection.
Overview Purpose Published metabolomic studies so far have involved less than 200 individual samp... more Overview Purpose Published metabolomic studies so far have involved less than 200 individual samples. Such surveys are accomplished within a week without too much drift of instrument sensitivity or retention time shifts. We show how quality control charts and standard operating procedures maintain high data quality even in larger programs. Equally important are the detection, alignment and annotation of individual deconvoluted peaks for over 1,000 chromatograms. If each deconvoluted 'signal' is taken into consideration, lists of target peaks expand to thousands of entries. We here demonstrate how severe constraints on mass spectral purity, s/n ratios and detection frequency manage unbiased metabolomics data in large scale experiments . Methods A Leco corp. Pegasus III GC-TOF was equipped with a dual arm CTC robotic derivatization station and an ATAS automatic liner exchange and direct thermodesorption injection device. Quality control was achieved by seven standard operating...
SUMMARY: Metabolomic publications and databases use different database identifiers or even trivia... more SUMMARY: Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including
Metabolomics is the methodology that identifies and measures global pools of small molecules (of ... more Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and transcriptomics. This paper describes the analysis of Arabidopsis metabolomics data sets acquired by a consortium that includes five analytical laboratories, bioinformaticists, and biostatisticians, which aims to develop and validate metabolomics as a hypothesis-generating functional genomics tool. The consortium is de...
The metabolite profile changes induced by Fe deficiency in leaves and xylem sap of several Strate... more The metabolite profile changes induced by Fe deficiency in leaves and xylem sap of several Strategy I plant species have been characterized. We have confirmed that Fe deficiency causes consistent changes both in the xylem sap and leaf metabolite profiles. The main changes in the xylem sap metabolite profile in response to Fe deficiency include consistent decreases in amino acids, N-related metabolites and carbohydrates, and increases in TCA cycle metabolites. In tomato, Fe resupply causes a transitory flush of xylem sap carboxylates, but within 1 day the metabolite profile of the xylem sap from Fe-deficient plants becomes similar to that of Fe-sufficient controls. The main changes in the metabolite profile of leaf extracts in response to Fe deficiency include consistent increases in amino acids and N-related metabolites, carbohydrates and TCA cycle metabolites. In leaves, selected pairs of amino acids and TCA cycle metabolites show high correlations, with the sign depending of the F...
Saccharophagus degradans is a potent degrader of marine and plant cell wall polysaccharides. In p... more Saccharophagus degradans is a potent degrader of marine and plant cell wall polysaccharides. In particular, it is capable of degrading and metabolizing agarose that is the main component of marine red algae. To understand its degradation and metabolism of agarose along with the agarase expression profile, S. degradans was grown using different carbon sources including galactose, agarose, glucose and cellulose. The metabolite profiling was conducted by using GC-TOF MS and in-house programmed database, BinBase. When the metabolite profiles of cells on galactose and agarose were compared, principal component analysis of 133 identified metabolites revealed clear separations between the groups on galactose and agarose. S. degradans grown on agarose was found to use different carbon catabolic pathways from that grown on other carbon sources. The metabolite profile of cells grown using galactose had increased abundances of glycerol, glycerol derivatives and fatty acids. The use of polysaccharides such as agarose or cellulose led to the increased abundances of amino acids and intermediates of nucleotide biosynthesis.
Iron homeostasis is an important process for flower development and plant fertility. The role of ... more Iron homeostasis is an important process for flower development and plant fertility. The role of plastids in these processes has been shown to be essential. To document the relationships between plastid iron homeostasis and flower biology further, a global study (transcriptome, proteome, metabolome, and hormone analysis) was performed of Arabidopsis flowers from wild-type and triple atfer1-3-4 ferritin mutant plants grown under iron-sufficient or excess conditions. Some major modifications in specific functional categories were consistently observed at these three omic levels, although no significant overlaps of specific transcripts and proteins were detected. These modifications concerned redox reactions and oxidative stress, as well as amino acid and protein catabolism, this latter point being exemplified by an almost 10-fold increase in urea concentration of atfer1-3-4 flowers from plants grown under iron excess conditions. The mutant background caused alterations in Fe-haem redox proteins located in membranes and in hormone-responsive proteins. Specific effects of excess Fe in the mutant included further changes in these categories, supporting the idea that the mutant is facing a more intense Fe/redox stress than the wild type. The mutation and/or excess Fe had a strong impact at the membrane level, as denoted by the changes in the transporter and lipid metabolism categories. In spite of the large number of genes and proteins responsive to hormones found to be regulated in this study, changes in the hormonal balance were restricted to cytokinins, especially in the mutant plants grown under Fe excess conditions.
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Papers by Gert Wohlgemuth