4.5 Article

COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA

Journal

PROTEOMICS
Volume 11, Issue 6, Pages 1064-1074

Publisher

WILEY
DOI: 10.1002/pmic.201000616

Keywords

Bioinformatics; Informatics; Protein identification; Protein quantitation; Software

Funding

  1. University of Washington's Proteomics Resource [UWPR95794]
  2. NIH [NIH 5T32HG002760, R01 GM080148, P01 GM081629]

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Here we present the Coon OMSSA Proteomic Analysis Software Suite (COMPASS): a free and open-source software pipeline for high-throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. We detail a synergistic set of tools for protein database generation, spectral reduction, peptide false discovery rate analysis, peptide quantitation via isobaric labeling, protein parsimony and protein false discovery rate analysis, and protein quantitation. We strive for maximum ease of use, utilizing graphical user interfaces and working with data files in the original instrument vendor format. Results are stored in plain text comma-separated value files, which are easy to view and manipulate with a text editor or spreadsheet program. We illustrate the operation and efficacy of COMPASS through the use of two LC-MS/MS data sets. The first is a data set of a highly annotated mixture of standard proteins and manually validated contaminants that exhibits the identification workflow. The second is a data set of yeast peptides, labeled with isobaric stable isotope tags and mixed in known ratios, to demonstrate the quantitative workflow. For these two data sets, COMPASS performs equivalently or better than the current de facto standard, the Trans-Proteomic Pipeline.

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