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Bioinformatics Advance Access first published online on June 1, 2007
This version published online on June 14, 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 , Nikola Tolic , Navdeep Jaitly , Jason L. Shaw , Joshua N. Adkins and Richard D. Smith *

Pacific Northwest National Laboratory, Richland, WA 99354 USA

*To whom correspondence should be addressed. Dr. Richard Smith, E-mail: rds{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/

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Alfonso Valencia

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

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