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.

Neuropeptidomics: MS Applied to the Discovery of Novel Peptides from the Brain

“…Accurately predicting all of the neuropeptides produced by a particular gene is difficult, because of the large variation in PTMs and the complex processing pattern that a peptide precursor undergoes while it is being proteolytically cleaved to a biologically active neuropeptide (47 ). Most software for peptide sequencing is designed for identification of enzymatically cleaved peptides and proteins.…”

High Identification Rates of Endogenous Neuropeptides from Mouse Brain

“…20,21 Database search was conducted against the Swepep mouse neuropeptide precursors database. 11 The Swepep precursor database was downloaded from www.swepep.org and loaded to Peaks studio 5.3 by using the UniprotKB/TrEMBL FASTA format and taxonomy options. Peaks Studio 5.3 was used for various functions such as Data Refinement, Auto De Novo, and Peaks Search (homology search).…”

“…5 A number of studies have addressed the discovery of as many neuropeptides as possible from brain samples by using various methods such as novel sample treatment methods, 6,7 derivatization, 4 two dimension separation, 8 high resolution MS, 9,10 and database construction. 11 This work has substantially improved the neuropeptide identification rate and greatly enlarged our knowledge of neuropeptides in brain. Previous single studies have generally been able to report around 50− 150 peptides, including but a few classical neuropeptides, regardless of whether the sample was prepared from a specific brain area or the whole brain.…”

Analysis of human serum phosphopeptidome by a focused database searching strategy

“…The focused database searching was demonstrated to be an effective approach to decrease false negatives and increase identification sensitivity [16,17,29,30]. For example, Ishihama et al built a focused database for analysis of phosphopeptides in Neuro2a Cell and mouse brain.…”

“…Several peptidome databases have been developed recently, such as PepBank [15] and SwePep [16,17]. PepBank is a database of peptide sequences and SwePep is a database of large collections of peptide spectra, both holding great potential in peptidome studies of many biological samples such as brain.…”