PatternLab is a tool for the analysis of proteomics data. The PatternLab package includes functions for formatting sequence databases, peptide spectrum matching, filtering and organizing, extraction of quantitative information from label-free and labeled data, statistics for differential proteomics, display of results in a variety of formats, similarity studies with de novo sequencing data, analysis of time-course experiments.
Proteomics; Proteomics experiment
Carvalho PC, Lima DB, Leprevost FV, Santos MD, Fischer JS, Aquino PF, Moresco JJ, Yates JR 3rd, Barbosa VC "Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0" Nat Protoc. 2016 Jan;11(1):102-17. https://doi.org/10.1038/nprot.2015.133
PMID: 26658470
PMCID: PMC5722229
Carvalho PC, Yates Iii JR, Barbosa VC "Analyzing shotgun proteomic data with PatternLab for proteomics" Current Protocols in Bioinformatics, v. Chapter 13, p. Unit 13.13 https://doi.org/10.1002/0471250953.bi1313s30
PMID: 20521246
PMCID: PMC2933420
Carvalho PC, Fischer JS, Xu T, Yates JR 3rd, Barbosa VC "PatternLab: from mass spectra to label-free differential shotgun proteomics" Curr Protoc Bioinformatics. 2012 Dec;Chapter 13:Unit13.19. https://doi.org/10.1002/0471250953.bi1319s40
PMID: 23255152
Carvalho PC, Fischer JS, Chen EI, Yates JR, Barbosa VC "PatternLab for proteomics: a tool for differential shotgun proteomics." BMC Bioinformatics 2008 https://doi.org/10.1186/1471-2105-9-316
PMID: 18644148
PMCID: PMC2488363
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