Glomerulopathies with nephrotic syndrome that are resistant to therapy often progress to end-stag... more Glomerulopathies with nephrotic syndrome that are resistant to therapy often progress to end-stage chronic kidney disease (CKD) and require timely and accurate diagnosis. Targeted quantitative urine proteome analysis by mass spectrometry (MS) with multiple-reaction monitoring (MRM) is a promising tool for early CKD diagnostics that could replace the invasive biopsy procedure. However, there are few studies regarding the development of highly multiplexed MRM assays for urine proteome analysis, and the two MRM assays for urine proteomics described so far demonstrate very low consistency. Thus, the further development of targeted urine proteome assays for CKD is actual task. Herein, a BAK270 MRM assay previously validated for blood plasma protein analysis was adapted for urine-targeted proteomics. Because proteinuria associated with renal impairment is usually associated with an increased diversity of plasma proteins being present in urine, the use of this panel was appropriate. Anothe...
The molecular mechanisms underlying cardiovascular complications after the SARS-CoV-2 infection r... more The molecular mechanisms underlying cardiovascular complications after the SARS-CoV-2 infection remain unknown. The goal of our study was to analyze the features of blood coagulation, platelet aggregation, and plasma proteomics in COVID-19 convalescents with AMI. The study included 66 AMI patients and 58 healthy volunteers. The groups were divided according to the anti-N IgG levels (AMI post-COVID (n = 44), AMI control (n = 22), control post-COVID (n = 31), and control (n = 27)). All participants underwent rotational thromboelastometry, thrombodynamics, impedance aggregometry, and blood plasma proteomics analysis. Both AMI groups of patients demonstrated higher values of clot growth rates, thrombus size and density, as well as the elevated levels of components of the complement system, proteins modifying the state of endothelium, acute-phase and procoagulant proteins. In comparison with AMI control, AMI post-COVID patients demonstrated decreased levels of proteins connected to infla...
ABSTRACT The physicochemical conditions of the aqueous environment at the dawn of biological evol... more ABSTRACT The physicochemical conditions of the aqueous environment at the dawn of biological evolution were of key importance for abiogenic peptide synthesis. Recently, we have shown theoretical and experimental evidence for the unique role of potassium ions in the exponential acceleration of undirected peptide synthesis from L-glutamic acid. These data have confirmed our previous hypothesis that the first protocell emerged in a potassium rather than sodium-rich aqueous solution (seawater). The present work provides experimental data for an interpretation of concentration dependence and of optimal effective concentration of potassium and sodium ions in L-glutamic acid peptide formation.
In carrying out proteomic researches using mass-spectrometry there often arises a need to compare... more In carrying out proteomic researches using mass-spectrometry there often arises a need to compare experimental data with each other (e.g. control of pathology, the labeled to unlabelled samples). If for peptide identification in different experiments one uses only their exact mass measurements and the retention time in the chromatographic column, difficulties with the identification of chromatographic peaks belonging to the same substances in different chromatograms come up (retention time normalization). Due to inevitable discrepancies in chromatographic conditions of experiments (replacement of chromatographic columns, small changes in mobile phase flow rate or solvent concentration) retention times of the same peptides will diverge from experiment to experiment. In this paper we offer a reliable method for selecting peaks from mass-chromatograms corresponding to the same peptides, which can later be used for retention time normalization (either linear or any other monotone functi...
Proteomic studies with the use of mass spectrometry required comparison of different experimental... more Proteomic studies with the use of mass spectrometry required comparison of different experimental data (for example, control with a pathology or labeled and unlabeled samples). Identification of chromatographic peaks of the same substance in different chromatograms (time normalization of chromatograms) is complicated if peptides are identified in different experiments according only to their exactly evaluated masses and retention times on
Journal of the American Society for Mass Spectrometry, 2014
Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T m... more Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T magnet using a dynamically harmonized Fourier transform ion cyclotron resonance (FT ICR) cell. Mass spectra of the fine structure of the isotopic distribution of a peptide were obtained and strong discrimination of small intensity peaks was observed in case of resonance excitation of the ions of the whole isotopic cluster to the same cyclotron radius. The absence of some peaks from the mass spectra of the fine structure was explained basing on results of computer simulations showing strong ion cloud interactions, which cause the coalescence of peaks with m/z close to that of the highest magnitude peak. The way to prevent peak discrimination is to excite ion clouds of different m/z to different cyclotron radii, which was demonstrated and investigated both experimentally and by computer simulations.
The urine protein composition (proteome) of healthy human was analyzed using proteomic techniques... more The urine protein composition (proteome) of healthy human was analyzed using proteomic techniques to obtain data in physiological condition and after six months space flights. It was shown that after long duration space flights in cosmonaut's urine reveals specific minor proteins which can be identified as proteins came from kidney and urinary tract.
We report an approach to study volatile organic compounds based on thermal desorption combined wi... more We report an approach to study volatile organic compounds based on thermal desorption combined with atmospheric pressure photo ionization. The approach allows the sequential evaporation of different fractions of the sample, which simplifies the mass spectrum. We have applied the developed method for the detection of petroleum in vegetable oil. We have shown that in the negative mode, ions of fatty acids corresponding to vegetable oil dominates, while in the positive mode under relatively low temperature the light fraction of petroleum rapidly evaporates making it easy detectable.
ABSTRACT Transthyretin, one of the major blood proteins, displays a variety of posttranslational ... more ABSTRACT Transthyretin, one of the major blood proteins, displays a variety of posttranslational modifications, including those related to the development of grave diseases, such as Alzheimer’s disease, and familial amyloid polyneuropathy. A combined analytical technique based on the use of two mass spectrometric approaches (bottom-up and top-down) has been developed in the present study to determine the role of the modified forms of transthyretin in the progression of Alzheimer’s disease. The high efficiency of this technique has been demonstrated for ten serum samples obtained from patients diagnosed with Alzheimer’s disease and healthy volunteers.
Glomerulopathies with nephrotic syndrome that are resistant to therapy often progress to end-stag... more Glomerulopathies with nephrotic syndrome that are resistant to therapy often progress to end-stage chronic kidney disease (CKD) and require timely and accurate diagnosis. Targeted quantitative urine proteome analysis by mass spectrometry (MS) with multiple-reaction monitoring (MRM) is a promising tool for early CKD diagnostics that could replace the invasive biopsy procedure. However, there are few studies regarding the development of highly multiplexed MRM assays for urine proteome analysis, and the two MRM assays for urine proteomics described so far demonstrate very low consistency. Thus, the further development of targeted urine proteome assays for CKD is actual task. Herein, a BAK270 MRM assay previously validated for blood plasma protein analysis was adapted for urine-targeted proteomics. Because proteinuria associated with renal impairment is usually associated with an increased diversity of plasma proteins being present in urine, the use of this panel was appropriate. Anothe...
The molecular mechanisms underlying cardiovascular complications after the SARS-CoV-2 infection r... more The molecular mechanisms underlying cardiovascular complications after the SARS-CoV-2 infection remain unknown. The goal of our study was to analyze the features of blood coagulation, platelet aggregation, and plasma proteomics in COVID-19 convalescents with AMI. The study included 66 AMI patients and 58 healthy volunteers. The groups were divided according to the anti-N IgG levels (AMI post-COVID (n = 44), AMI control (n = 22), control post-COVID (n = 31), and control (n = 27)). All participants underwent rotational thromboelastometry, thrombodynamics, impedance aggregometry, and blood plasma proteomics analysis. Both AMI groups of patients demonstrated higher values of clot growth rates, thrombus size and density, as well as the elevated levels of components of the complement system, proteins modifying the state of endothelium, acute-phase and procoagulant proteins. In comparison with AMI control, AMI post-COVID patients demonstrated decreased levels of proteins connected to infla...
ABSTRACT The physicochemical conditions of the aqueous environment at the dawn of biological evol... more ABSTRACT The physicochemical conditions of the aqueous environment at the dawn of biological evolution were of key importance for abiogenic peptide synthesis. Recently, we have shown theoretical and experimental evidence for the unique role of potassium ions in the exponential acceleration of undirected peptide synthesis from L-glutamic acid. These data have confirmed our previous hypothesis that the first protocell emerged in a potassium rather than sodium-rich aqueous solution (seawater). The present work provides experimental data for an interpretation of concentration dependence and of optimal effective concentration of potassium and sodium ions in L-glutamic acid peptide formation.
In carrying out proteomic researches using mass-spectrometry there often arises a need to compare... more In carrying out proteomic researches using mass-spectrometry there often arises a need to compare experimental data with each other (e.g. control of pathology, the labeled to unlabelled samples). If for peptide identification in different experiments one uses only their exact mass measurements and the retention time in the chromatographic column, difficulties with the identification of chromatographic peaks belonging to the same substances in different chromatograms come up (retention time normalization). Due to inevitable discrepancies in chromatographic conditions of experiments (replacement of chromatographic columns, small changes in mobile phase flow rate or solvent concentration) retention times of the same peptides will diverge from experiment to experiment. In this paper we offer a reliable method for selecting peaks from mass-chromatograms corresponding to the same peptides, which can later be used for retention time normalization (either linear or any other monotone functi...
Proteomic studies with the use of mass spectrometry required comparison of different experimental... more Proteomic studies with the use of mass spectrometry required comparison of different experimental data (for example, control with a pathology or labeled and unlabeled samples). Identification of chromatographic peaks of the same substance in different chromatograms (time normalization of chromatograms) is complicated if peptides are identified in different experiments according only to their exactly evaluated masses and retention times on
Journal of the American Society for Mass Spectrometry, 2014
Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T m... more Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T magnet using a dynamically harmonized Fourier transform ion cyclotron resonance (FT ICR) cell. Mass spectra of the fine structure of the isotopic distribution of a peptide were obtained and strong discrimination of small intensity peaks was observed in case of resonance excitation of the ions of the whole isotopic cluster to the same cyclotron radius. The absence of some peaks from the mass spectra of the fine structure was explained basing on results of computer simulations showing strong ion cloud interactions, which cause the coalescence of peaks with m/z close to that of the highest magnitude peak. The way to prevent peak discrimination is to excite ion clouds of different m/z to different cyclotron radii, which was demonstrated and investigated both experimentally and by computer simulations.
The urine protein composition (proteome) of healthy human was analyzed using proteomic techniques... more The urine protein composition (proteome) of healthy human was analyzed using proteomic techniques to obtain data in physiological condition and after six months space flights. It was shown that after long duration space flights in cosmonaut's urine reveals specific minor proteins which can be identified as proteins came from kidney and urinary tract.
We report an approach to study volatile organic compounds based on thermal desorption combined wi... more We report an approach to study volatile organic compounds based on thermal desorption combined with atmospheric pressure photo ionization. The approach allows the sequential evaporation of different fractions of the sample, which simplifies the mass spectrum. We have applied the developed method for the detection of petroleum in vegetable oil. We have shown that in the negative mode, ions of fatty acids corresponding to vegetable oil dominates, while in the positive mode under relatively low temperature the light fraction of petroleum rapidly evaporates making it easy detectable.
ABSTRACT Transthyretin, one of the major blood proteins, displays a variety of posttranslational ... more ABSTRACT Transthyretin, one of the major blood proteins, displays a variety of posttranslational modifications, including those related to the development of grave diseases, such as Alzheimer’s disease, and familial amyloid polyneuropathy. A combined analytical technique based on the use of two mass spectrometric approaches (bottom-up and top-down) has been developed in the present study to determine the role of the modified forms of transthyretin in the progression of Alzheimer’s disease. The high efficiency of this technique has been demonstrated for ten serum samples obtained from patients diagnosed with Alzheimer’s disease and healthy volunteers.
Uploads
Papers by Evgeny N Nikolaev