PASSEL: The PeptideAtlas SRMexperiment library
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
Search for more papers by this authorRichard Kreisberg
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorDavid S. Campbell
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorUlrike Kusebauch
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorMi-Youn Brusniak
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorRuth Hüttenhain
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
Search for more papers by this authorRalph Schiess
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
Search for more papers by this authorNathalie Selevsek
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
Search for more papers by this authorRuedi 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
Search for more papers by this authorRobert L. Moritz
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorCorresponding 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
Search for more papers by this authorRichard Kreisberg
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorDavid S. Campbell
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorUlrike Kusebauch
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorMi-Youn Brusniak
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorRuth Hüttenhain
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
Search for more papers by this authorRalph Schiess
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
Search for more papers by this authorNathalie Selevsek
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
Search for more papers by this authorRuedi 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
Search for more papers by this authorRobert L. Moritz
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorAbstract
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.
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