Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0
This protocol describes PatternLab 4.0, an integrated software environment for the analysis of shotgun proteomics data. PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for the analysis of shotgun proteomic data. The contained mod...
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| Veröffentlicht in: | Nature protocols 2016-01, Vol.11 (1), p.102-117 |
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| creator | Carvalho, Paulo C Lima, Diogo B Leprevost, Felipe V Santos, Marlon D M Fischer, Juliana S G Aquino, Priscila F Moresco, James J Yates, John R Barbosa, Valmir C |
| description | This protocol describes PatternLab 4.0, an integrated software environment for the analysis of shotgun proteomics data.
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
. |
| doi_str_mv | 10.1038/nprot.2015.133 |
| format | Article |
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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
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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
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software environment for the analysis of shotgun proteomics data.
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
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| subjects | 631/114/2784 631/1647/2067 631/45/475 639/638/11/296 82/58 Analytical Chemistry Biological Techniques Computational biology Computational Biology/Bioinformatics Computer applications Data analysis Databases, Protein Humans Innovations Integrated software Life Sciences Mass spectra Medical equipment Microarrays Modules Organic Chemistry Peptides - chemistry Peptides - metabolism Physiological apparatus Protein Processing, Post-Translational Proteomics Proteomics - methods protocol Shotguns Software Statistical analysis Systems Integration Tandem Mass Spectrometry Time Factors |
| title | Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0 |
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