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Bioinformatics Advance Access published online on September 19, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn491
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MS-BID: a Java package for label-free LC-MS based comparative proteomic analysis

Daehee Hwang 1,2,¶,*, Ning Zhang 1,¶, Hookeun Lee 1,3, Eugene Yi 1, Hui Zhang 1, Inyoul Y. Lee 1, Leroy Hood 1 and Ruedi Aebersold 1,4,5

1Institute for Systems Biology, Seattle, WA 98103, USA, 2I-BIO Program and Department of Chemical Eng., Pohang, 790-784, Republic of Korea, 3LCDI, Gachon University of Medicine and Science, Incheon, Republic of Korea, 4Institute for Molecular Systems Biology, ETH, CH-8093 Zürich and 5Faculty of natural science, University of Zürich, Switzerland.

*To whom correspondence should be addressed. Dr. Daehee Hwang, E-mail: dhhwang{at}postech.ac.kr


  Abstract

Summary: MS-BID (MS Biomarker Discovery Platform) is an integrative computational pipeline for biomarker discovery using LC-MS based comparative proteomic analysis. This platform consists of several computational tools for 1) detecting peptides in the collected patterns; 2) matching detected peptides across a number of LC-MS datasets; and 3) selecting discriminatory peptides between classes of samples.

Availability: MS-BID source codes, binaries and documentations are freely available under LGPL from http://tools.proteomecen-ter.org/msBID.php

Contact: dhhwang{at}postech.ac.kr

Associate Editor: Prof. John Quackenbush

Authors contributed equally to this work and should be considered as first authors

Received on May 25, 2008; revised on September 2, 2008; accepted on September 12, 2008

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