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Bioinformatics Advance Access originally published online on January 6, 2009
Bioinformatics 2009 25(5):682-683; doi:10.1093/bioinformatics/btp005
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Prequips—an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data

Nils Gehlenborg 1,2,3, Wei Yan 1, Inyoul Y. Lee 1, Hyuntae Yoo 1, Kay Nieselt 2, Daehee Hwang 1,4,5,*, Ruedi Aebersold 1,6 and Leroy Hood 1

1Institute for Systems Biology, Seattle, USA, 2Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK, 4I-Bio Program, 5Department of Chemical Engineering, POSTECH, Pohang, Republic of Korea and 6Institute for Molecular Systems Biology, ETH and Faculty of Natural Science, University of Zürich, Zürich, Switzerland

*To whom correspondence should be addressed.


  Abstract

Summary: We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies.

Availability: http://prequips.sourceforge.net

Contact: dhhwang{at}postech.ac.kr

Associate Editor: John Quackenbush

Received on October 19, 2008; revised on December 18, 2008; accepted on December 30, 2008

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