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Bioinformatics Advance Access published online on April 23, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn139
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

swissPIT: A novel approach for pipelined analysis of mass spectrometry data

Andreas Quandt 1,*, Patricia Hernandez 1, Alexandre Masselot 1,3, Céline Hernandez 1, Sergio Maffioletti 4, Cesare Pautasso 5, Ron D. Appel 1,2 and Frederique Lisacek 1

1 Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland
2 University of Geneva, Computer Science Department, Geneva, Switzerland
3 Geneva Bioinformatics (GeneBio) S.A., Geneva, Switzerland
4 Swiss National Supercomputing Centre, Manno, Switzerland
5 University of Lugano, Faculty of Informatics, Lugano, Switzerland

*To whom correspondence should be addressed. Andreas Quandt, E-mail: andreas.quandt{at}isb-sib.ch


  Abstract

The identification and characterisation of peptides from tandem mass spectrometry (MS/MS) data represents a critical aspect of proteomics. Today, tandem mass spectrometry analysis is often performed by only using a single identification program achieving identification rates between 10 – 50 % (Elias and Gygi, 2007). Be-side the development of new analysis tools, recent publications describe also the pipelining of different search programs to increase the identification rate (Keller et al., 2005, Hartler et al., 2007).

The swissPIT (Swiss Protein Identification Toolbox) follows this approach but goes a step further by providing the user an expand-able multi-tool platform capable of executing workflows to analyze Tandem MS-based data. One of the major problems in proteomics is the absent of standardized workflows to analyze the produced data. This includes the pre-processing part as well as the final identifica-tion of peptides and proteins. The main idea of swissPIT is not only the usage of different identification tool in parallel but also the mean-ingful concatenation of different identification strategies at the same time. The swissPIT is open source software but we also provide a user-friendly web platform, which demonstrates the capabilities of our software and which is available at http://swisspit.cscs.ch upon request for account.

Associate Editor: Dr. Jonathan Wren

Received on March 14, 2008; revised on April 10, 2008; accepted on April 10, 2008

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