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Bioinformatics Advance Access originally published online on March 20, 2009
Bioinformatics 2009 25(10):1341-1343; doi:10.1093/bioinformatics/btp155
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Automated diagnosis of LC-MS/MS performance

Hua Xu 1,* and Michael A. Freitas 2,*

1Proteomics and Informatics Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, IL 60612 and 2Department of Molecular Virology, Immunology and Medical Genetics, the Ohio State University, Columbus, OH 43210, USA

*To whom correspondence should be addressed.


  Abstract

Summary: We report a software scheme for automated diagnosis of liquid chromatography tandem mass spectrometry (LC-MS/MS) system performance. The proposed software scheme provides a robust framework for establishing automated diagnosis of LC-MS/MS system performance for a variety of instruments and experiments. This schematic consists of four main software components: (i) data conversion, (ii) peptide identification, (iii) LC retention time analysis and (iv) system performance evaluation. The implementation of a standard approach for assessing LC-MS/MS system performance enables researchers to apply reliable metrics to assess their workflows performance over different batch experiments. Furthermore, the results from system diagnosis can provide feedback to the workflow to stop batch analysis if system performance falls below prescribed thresholds. A basic implementation of the approach based on the MassMatrix database search and LC retention time analysis programs is presented.

Availability: An open source implementation of the LC-MS/MS system diagnosis software based on the MassMatrix database search program is freely available to non-commercial users and can be downloaded at www.massmatrix.net.

Contact: huaxu{at}uic.edu; freitas.5{at}osu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Jonathan Wren

Received on December 1, 2008; revised on February 21, 2009; accepted on March 15, 2009

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