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Crux: rapid open source protein tandem mass spectrometry analysis
Journal of Proteome Research. 2014. Vol. 13. No. 10. P. 4488–4491.
Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a crossplatform suite of analysis tools for interpreting protein mass spectrometry data.
Keywords: mass spectrometry
Petrova D., Biomolecules 2025
Added: January 18, 2026
Blokhin V., Shupik M., Gutner U. et al., Biomolecules 2022 Vol. 12 No. 1 Article 93
Parkinson’s disease (PD) is a neurodegenerative disease incurable due to late diagnosis and treatment. Therefore, one of the priorities of neurology is to study the mechanisms of PD pathogenesis at the preclinical and early clinical stages. Given the important role of sphingolipids in the pathogenesis of neurodegenerative diseases, we aimed to analyze the gene expression ...
Added: March 4, 2024
Danilova Yulia, Voronkova Anastasia, Sulimov Pavel et al., Journal of Proteome Research 2019 Vol. 18 No. 5 P. 2354–2358
Accurate target-decoy-based false discovery rate (FDR) control of peptide identification from tandem mass-spectrometry data relies on an important but often neglected assumption that incorrect spectrum annotations are equally likely to receive either target or decoy peptides. Here we argue that this assumption is often violated in practice, even by popular methods. Preference can be given ...
Added: October 6, 2021
Ovchinnikova K., Lachlan S., Rakhlin A. et al., Bioinformatics 2020 P. 1–10
Motivation
Imaging mass spectrometry (imaging MS) is a prominent technique for capturing distributions of molecules in tissue sections. Various computational methods for imaging MS rely on quantifying spatial correlations between ion images, referred to as co-localization. However, no comprehensive evaluation of co-localization measures has ever been performed; this leads to arbitrary choices and hinders method development.
Results
We ...
Added: March 15, 2020
Vladimir A. Korshun, Analytical Methods 2017 Vol. 9 No. 45 P. 6335–6340
The derivatization reagent was prepared in situ by the reaction of tris(2,6-dimethoxyphenyl)methylium hexafluorophosphate with N-(2- aminoethyl)maleimide and used for the modification of a number of low molecular weight thiols. The adducts were analyzed by (MA)(NA) LDI MS and ESI MS. All registered mass spectra ((MA)(NA)LDI, ESI) revealed intense peaks of the cations of the derivatization products. The increment of the derivatization agent ...
Added: November 8, 2019
Petushkova N., Zgoda V., Pyatnitskiy M. et al., Plos One 2017 Vol. 12 No. 5 P. 0177427-1–0177427-21
Liquid chromatography-tandem mass spectrometry was used to analyze plasma proteins of volunteers (control) and patients with glioblastoma multiform (GBM). A database search was pre-set with a variable post-translational modification (PTM): phosphorylation, acetylation or ubiquitination. There were no significant differences between the control and the GBM groups regarding the number of protein identifications, sequence coverage or number of PTMs. However, in GBM plasma, we unambiguously observed a decreased fraction in post-translationally modified peptides ...
Added: March 14, 2018
Kuznetsova K., Trufanov P., Moysa A. et al., Rapid Communications in Mass Spectrometry 2016 Vol. 30 No. 11 P. 1323–1331
One of the problems in proteogenomic research aimed at identification of variant peptides is the presence of peptides with amino acid isomers of different origin in the analyzed samples. Among the most challenging examples are peptides with threonine and isothreonine (homoserine) in their sequences. Indeed, the latter residue may appear in vitro as a methionine substitution during sample preparation for shotgun proteome analysis. Yet, this substitution of ...
Added: March 14, 2018
Palmer A., Phapale P., Chernyavsky I. et al., Nature Methods 2017 No. 14 P. 57–60
High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for ...
Added: February 7, 2017
Kertesz-Farkas A., Myers M. P., Current Bioinformatics 2012 Vol. 7 No. 2 P. 221–230
Bottom-up proteomics (mass spectrometry analysis of peptides obtained by proteolysis and separated by liquid chromatography, (LCMS/MS)) is one of the most frequently used techniques for identifying and characterizing proteins in biological samples. A key element of the analysis is database searching when the mass spectra of the peptides are compared with a database of theoretically ...
Added: November 18, 2015
Kertesz-Farkas A., Myers M. P., Protein and peptide letters 2014 Vol. 21 No. 8 P. 858–863
Identification and elimination of noise peaks in mass spectra from large proteomics data streams simultaneously improves the accuracy of peptide identification and significantly decreases the size of the data. There are a number of peak filtering strategies that can achieve this goal. Here we present a simple algorithm wherein the number of highest intensity peaks ...
Added: November 18, 2015
Kertesz-Farkas A., Myers M. P., Current Bioinformatics 2012 Vol. 7 No. 2 P. 212–220
Mass spectrometry based proteomics analysis can produce many thousands of spectra in a single experiment, and much of this data, frequently greater than 50%, cannot be properly evaluated computationally. Therefore a number of strategies have been developed to aid the processing of mass spectra and typically focus on the identification and elimination of noise, which ...
Added: November 18, 2015
Kertesz-Farkas A., Keich U., Noble W., Journal of Proteome Research 2015 Vol. 14 No. 8 P. 3148–3161
Interpreting the potentially vast number of hypotheses generated by a shotgun proteomics experiment requires a valid and accurate procedure for assigning statistical confidence estimates to the identified tandem mass spectra. Despite the crucial role such procedures play in most highthroughput proteomics experiments, the scientific literature has not reached a consensus about the best confidence estimation ...
Added: November 18, 2015
Alexandrov T., Chernyavsky I., Becker M. et al., Analytical Chemistry 2013 Vol. 85 No. 23 P. 11189–11195
Imaging mass spectrometry (imaging MS) has emerged in the past decade as a label-free, spatially resolved, and multipurpose bioanalytical technique for direct analysis of biological samples from animal tissue, plant tissue, biofilms, and polymer films. Imaging MS has been successfully incorporated into many biomedical pipelines where it is usually applied in the so-called untargeted mode-capturing spatial localization of a multitude of ions ...
Added: November 18, 2013