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Bioinformatics Advance Access published online on June 1, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm281
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

VIPER: an advanced software package to support high-throughput LC-MS peptide identification

Matthew E. Monroe 1, Nikola Tolic 1, Navdeep Jaitly 1, Jason L. Shaw 1, Joshua N. Adkins 1 and Richard D. Smith 1,*

1Pacific Northwest National Laboratory,{dagger}, Richland, WA 99354 USA

*To whom correspondence should be addressed. Dr. Richard Smith, E-mail: rds{at}pnl.gov, kelly.sandretto{at}pnl.gov


  Abstract

Summary: The Accurate Mass and Time (AMT) tag approach is used for analysis of large scale experiments by combining information generated over multiple datasets and instrument types. The VIPER software package is one of the key components of the data processing pipeline and implements automated algorithms to discover LC-MS features, align and match these LC-MS features to a database of peptides previously identified in LC-MS/MS analyses, and identify and quantify pairs of isotopically labeled peptides.

Availability: VIPER may be downloaded free of charge by registering at http://ncrr.pnl.gov/software/

Associate Editor: Prof. Alfonso Valencia

{dagger}This manuscript has been authored by Battelle Memorial Institute, Pacific Northwest Division, under Contract No. DE-AC05-76RL0 1830 with the U.S. Department of Energy. By accepting the article for publication, the publisher acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

Received on January 16, 2007; revised on May 17, 2007; accepted on May 18, 2007

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