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Originally published In Press as doi:10.1074/mcp.T400004-MCP200 on July 29, 2004.
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Molecular & Cellular Proteomics 3:1023-1038, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

Technology

Experimental Peptide Identification Repository (EPIR)

An Integrated Peptide-Centric Platform for Validation and Mining of Tandem Mass Spectrometry Data*,S

Dan Bach Kristensen{ddagger},§, Jan Christian Brønd§, Peter Aagaard Nielsen, Jens Roswald Andersen, Ole Tang Sørensen, Vibeke Jørgensen, Kenneth Budin, Jesper Matthiesen, Peter Venø, Hans Mikael Jespersen, Christian H. Ahrens, Soeren Schandorff, Peder Thusgaard Ruhoff, Jacek R. Wisniewski, Keiryn L. Bennett and Alexandre V. Podtelejnikov

From MDS Inc., Denmark, Staermosegaardsvej 6, DK-5230 Odense M, Denmark

LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can be parsed into EPIR and subsequently validated and mined using a set of software modules that overlay the database. These include a peptide validation module, a protein grouping module, a generic module for extracting quantitative data, a comparative module, and additional modules for extracting statistical information. In the present study, the utility of EPIR and associated software tools is demonstrated on LC MS/MS data derived from a set of model proteins and complex protein mixtures derived from MCF-7 breast cancer cells. Emphasis is placed on the key strengths of EPIR, including the ability to validate and mine multiple combined datasets, and presentation of protein-level evidence in concise, nonredundant protein groups that are based on shared peptide evidence.

{ddagger} To whom correspondence should be addressed: MDS Inc., Denmark, Staermosegaardsvej 6, DK-5230 Odense M, Denmark. Tel.: 45- 33262013; Fax: 45-65572001; E-mail: dkristensen{at}mdsdenmark.com


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