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Bioinformatics Advance Access published online on September 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm467
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TandTRAQ: An open-source tool for integrated protein identification and quantitation

Ted Laderas 1,2,*, Cory Bystrom 3, Debra McMillen 3, Guang Fan 4 and Shannon McWeeney 1,2

1Informatics Shared Resource, OHSU Cancer Institute, Oregon Health & Science University, Portland Oregon, USA 97212. 2Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon 3Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon, 4Department of Anatomical Pathology, Oregon Health & Science University, Portland, Oregon

*To whom correspondence should be addressed. Mr. Ted Laderas, E-mail: laderast{at}ohsu.edu


  Abstract

Summary: Integrating qualitative protein identification with quantiative protein analysis is nontrivial, given incompatibility in output formats. We present TandTRAQ, a standalone utility that integrates results from i-Tracker, an open-source iTRAQ quantitation program with the search results from X!Tandem, an open source proteome search engine. The utility runs from the command-line and can be easily integrated into a pipeline for automation.

Availability: The TandTRAQ Perl scripts are freely available for download at http://www.ohsucancer.com/isrdev/tandtraq/

Contact: laderast{at}ohsu.edu

Associate Editor: Prof. Anna Tramontano

Received on July 18, 2007; revised on August 30, 2007; accepted on September 8, 2007

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