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Proteomics. 2011 Mar;11(6):1064-74. doi: 10.1002/pmic.201000616. Epub 2011 Feb 7.

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

Author information

1
Department of Chemistry, University of Wisconsin, Madison, WI, USA.

Abstract

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.

PMID:
21298793
PMCID:
PMC3049964
DOI:
10.1002/pmic.201000616
[Indexed for MEDLINE]
Free PMC Article

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