title: Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0.
abstract: PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for the analysis of shotgun proteomic data. The contained modules allow for formatting of sequence databases, peptide spectrum matching, statistical filtering and data organization, extracting quantitative information from label-free and chemically labeled data, and analyzing statistics for differential proteomics. PatternLab also has modules to perform similarity-driven studies with de novo sequencing data, to evaluate time-course experiments and to highlight the biological significance of data with regard to the Gene Ontology database. The PatternLab for proteomics 4.0 package brings together all of these modules in a self-contained software environment, which allows for complete proteomic data analysis and the display of results in a variety of graphical formats. All updates to PatternLab, including new features, have been previously tested on millions of mass spectra. PatternLab is easy to install, and it is freely available from http://patternlabforproteomics.org.
authors.affiliation: Computational Mass Spectrometry Group, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil.|Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
authors.forename: Paulo C
authors.initials: PC
authors.lastname: Carvalho
authors.affiliation: Computational Mass Spectrometry Group, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil.
authors.forename: Diogo B
authors.initials: DB
authors.lastname: Lima
authors.affiliation: Computational Mass Spectrometry Group, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil.|Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Felipe V
authors.identifier: http://orcid.org/0000-0002-8228-5374
authors.initials: FV
authors.lastname: Leprevost
authors.affiliation: Computational Mass Spectrometry Group, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil.
authors.forename: Marlon D M
authors.initials: MD
authors.lastname: Santos
authors.affiliation: Computational Mass Spectrometry Group, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil.
authors.forename: Juliana S G
authors.initials: JS
authors.lastname: Fischer
authors.affiliation: Leonidas e Maria Deane Institute, Fiocruz Amazonas, Manaus, Brazil.
authors.forename: Priscila F
authors.initials: PF
authors.lastname: Aquino
authors.affiliation: Laboratory for Biological Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: James J
authors.initials: JJ
authors.lastname: Moresco
authors.affiliation: Laboratory for Biological Mass Spectrometry, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: John R
authors.identifier: http://orcid.org/0000-0001-5267-1672
authors.initials: JR
authors.lastname: Yates
authors.affiliation: Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Valmir C
authors.identifier: http://orcid.org/0000-0003-1010-7170
authors.initials: VC
authors.lastname: Barbosa
mesh_terms: D030562:Databases, Protein; D006801:Humans; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D012984:Software; D018511:Systems Integration; D053719:Tandem Mass Spectrometry; D013997:Time Factors
chemical_list: D010455:Peptides