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Bioinformatics Advance Access originally published online on September 25, 2007
Bioinformatics 2007 23(24):3394-3396; doi:10.1093/bioinformatics/btm467
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

*To whom correspondence should be addressed.


  Abstract

Summary: Integrating qualitative protein identification with quantitative protein analysis is non-trivial, 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: Anna Tramontano

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

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