What is PatternLab?

PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data. PatternLab contains modules for formatting sequence databases, performing peptide spectrum matching, statistically filtering and organizing shotgun proteomic data, extracting quantitative information from label-free and chemically labeled data, performing statistics for differential proteomics, displaying results in a variety of graphical formats, performing similarity-driven studies with de novo sequencing data, and analyzing time-course experiments. Here, we present PatternLab for Proteomics V, which closely knits together all these modules in a self-contained environment, covering the principal aspects of proteomic data analysis as freely available and easily installable software.PatternLab is user-friendly, simple and provides a graphical user interface.

Please cite:

doi> “Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0”, Nature Protocols (11), 102-117, 2016.

What's New?

PatternLab V represents a leap in user experience.

Paulo C. Carvalho Researcher

References

doi> "PatternLab for proteomics: a tool for differential shotgun proteomics.", BMC bioinformatics, v. 9, p. 316, 2008.

doi> “Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0”, Nature Protocols (11), 102-117, 2016.

doi> “Simple, efficient, and thorough shotgun proteomic analysis with PatternLab for proteomics V” (Submitted)

EXAMPLE DATASET

Example dataset can be download here.

Search Comet - Peptide Spectrum Matching

Filter SEPro - Search Engine Processor

Please refer to our protocol for downstream bioinformatic analysis.

COLLABORATORS

IMPORTANT LINKS

UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information.

A public repository of protein and peptide identifications for the proteomics community.