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Molecular & Cellular Proteomics 5:998-1005, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

SwePep, a Database Designed for Endogenous Peptides and Mass Spectrometry^*

Maria Fälth^,, Karl Sköld^,, Mathias Norrman, Marcus Svensson^,, David Fenyö^|| and Per E. Andren^,,**

From the Laboratory for Biological and Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden, the Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, SE-75124 Uppsala, Sweden, and ^|| The Rockefeller University, New York, New York 10021

A new database, SwePep, specifically designed for endogenous peptides, has been constructed to significantly speed up the identification process from complex tissue samples utilizing mass spectrometry. In the identification process the experimental peptide masses are compared with the peptide masses stored in the database both with and without possible post-translational modifications. This intermediate identification step is fast and singles out peptides that are potential endogenous peptides and can later be confirmed with tandem mass spectrometry data. Successful applications of this methodology are presented. The SwePep database is a relational database developed using MySql and Java. The database contains 4180 annotated endogenous peptides from different tissues originating from 394 different species as well as 50 novel peptides from brain tissue identified in our laboratory. Information about the peptides, including mass, isoelectric point, sequence, and precursor protein, is also stored in the database. This new approach holds great potential for removing the bottleneck that occurs during the identification process in the field of peptidomics. The SwePep database is available to the public.

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