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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.
Язык:
английский
Ключевые слова: mass spectrometry
Blokhin V., Shupik M., Gutner U. и др., Biomolecules 2022 Vol. 12 No. 1 Article 93
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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 ...
Добавлено: 7 февраля 2017 г.
Кертес-Фаркаш А., 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 ...
Добавлено: 18 ноября 2015 г.
Кертес-Фаркаш А., 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 ...
Добавлено: 18 ноября 2015 г.
Кертес-Фаркаш А., 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 ...
Добавлено: 18 ноября 2015 г.
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 ...
Добавлено: 18 ноября 2015 г.
Alexandrov T., Chernyavsky I., Becker M. и др., Analytical Chemistry 2013 Vol. 85 No. 23 P. 11189–11195
Добавлено: 18 ноября 2013 г.