title: SwePep, a database designed for endogenous peptides and mass spectrometry.
abstract: 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.
authors.affiliation: Laboratory for Biological and Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden.
authors.forename: Maria
authors.initials: M
authors.lastname: Fälth
authors.forename: Karl
authors.initials: K
authors.lastname: Sköld
authors.forename: Mathias
authors.initials: M
authors.lastname: Norrman
authors.forename: Marcus
authors.initials: M
authors.lastname: Svensson
authors.forename: David
authors.initials: D
authors.lastname: Fenyö
authors.forename: Per E
authors.initials: PE
authors.lastname: Andren
mesh_terms: D000818:Animals; D030562:Databases, Protein; D006728:Hormones / Q000737:chemistry; D007031:Hypothalamus / Q000737:chemistry; D020407:Internet; D051379:Mice; D008810:Mice, Inbred C57BL; D009419:Nerve Tissue Proteins / Q000737:chemistry; D009479:Neuropeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry* / Q000145:classification*; D011499:Protein Processing, Post-Translational; D051381:Rats; D017207:Rats, Sprague-Dawley; D021241:Spectrometry, Mass, Electrospray Ionization
chemical_list: D006728:Hormones; D009419:Nerve Tissue Proteins; D009479:Neuropeptides; C489091:Pcp4 protein, mouse; D010455:Peptides