Volume 12, Issue 8 p. 1170-1175
Technical Brief

PASSEL: The PeptideAtlas SRMexperiment library

Terry Farrah

Terry Farrah

Institute for Systems Biology, Seattle, WA, USA

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Eric W. Deutsch

Corresponding Author

Eric W. Deutsch

Institute for Systems Biology, Seattle, WA, USA

Correspondence: Dr. Eric W. Deutsch, Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA

E-mail: [email protected]

Fax: +1-206-732-1299

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Richard Kreisberg

Richard Kreisberg

Institute for Systems Biology, Seattle, WA, USA

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Zhi Sun

Zhi Sun

Institute for Systems Biology, Seattle, WA, USA

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David S. Campbell

David S. Campbell

Institute for Systems Biology, Seattle, WA, USA

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Luis Mendoza

Luis Mendoza

Institute for Systems Biology, Seattle, WA, USA

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Ulrike Kusebauch

Ulrike Kusebauch

Institute for Systems Biology, Seattle, WA, USA

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Mi-Youn Brusniak

Mi-Youn Brusniak

Institute for Systems Biology, Seattle, WA, USA

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Ruth Hüttenhain

Ruth Hüttenhain

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

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Ralph Schiess

Ralph Schiess

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland

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Nathalie Selevsek

Nathalie Selevsek

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland

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Ruedi Aebersold

Ruedi Aebersold

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland

Faculty of Science, University of Zurich, Zurich, Switzerland

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Robert L. Moritz

Robert L. Moritz

Institute for Systems Biology, Seattle, WA, USA

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First published: 09 February 2012
Citations: 188

Abstract

Public repositories for proteomics data have accelerated proteomics research by enabling more efficient cross-analyses of datasets, supporting the creation of protein and peptide compendia of experimental results, supporting the development and testing of new software tools, and facilitating the manuscript review process. The repositories available to date have been designed to accommodate either shotgun experiments or generic proteomic data files. Here, we describe a new kind of proteomic data repository for the collection and representation of data from selected reaction monitoring (SRM) measurements. The PeptideAtlas SRM Experiment Library (PASSEL) allows researchers to easily submit proteomic data sets generated by SRM. The raw data are automatically processed in a uniform manner and the results are stored in a database, where they may be downloaded or browsed via a web interface that includes a chromatogram viewer. PASSELenables cross-analysis of SRMdata, supports optimization of SRMdata collection, and facilitates the review process of SRMdata. Further, PASSELwill help in the assessment of proteotypic peptide performance in a wide array of samples containing the same peptide, as well as across multiple experimental protocols.