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.
Highlights
A new database, SwePep, designed for endogenous peptides, has been constructed to significantly speed up the identification process from complex tissue samples utilizing mass spectrometry
The SwePep database currently consists of 4180 endogenous peptides. 4136 of them have been found in UniProt Knowledgebase, and the rest have been identified in our laboratory
The endogenous peptides will not contain many, if any, of such cleavage sites because they are processed at other specific sites by processing enzymes that release the bioactive peptide from the precursor and because of their small number of amino acid residues
Summary
SwePep is a Java [11] Enterprise Edition (J2EE) application implemented according to a multitier application model [12] It consists of a dynamic web interface, a relational database, and a business tier, which uses the client input from the web interface to construct and execute queries to the database. The web interface was developed using hypertext markup language (HTML), and the dynamic content was developed using Java ServerPages (JSP), which at runtime compiles to JavaServlets. This makes it possible for the web interface to communicate with the server side functions and the database. After the request is processed the control servlet sends a response back to the web interface, and the result of the request is displayed to the user
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