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Bioinformatics Advance Access published online on November 22, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl583
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 10, 2006
Accepted November 15, 2006

Applications note

PrepMS: TOF MS data graphical preprocessing tool

Yuliya V. Karpievitch 1 *, Elizabeth G. Hill 2, Adam J. Smolka 3, Jeffrey S. Morris 4, Kevin R. Coombes 4, Keith A. Baggerly 4, and Jonas S. Almeida 4

1 Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC, 29425; Department of Biostatistics and Applied Mathematics, M. D. Anderson Cancer Center, University of Texas, Houston, TX, 77030
2 Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC, 29425
3 Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425
4 Department of Biostatistics and Applied Mathematics, M. D. Anderson Cancer Center, University of Texas, Houston, TX, 77030

* To whom correspondence should be addressed.
Yuliya V. Karpievitch, E-mail: ykarpi{at}mdanderson.org


  Abstract

Summary: We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings experimentally determined to work well in most situations. These values can be changed by the user if desired. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection, and visual data quality assessment.

Availability: Stand-alone executable files and Matlab toolbox are available for download at: http://sourceforge.net/projects/prepms.

Associate Editor: Limsoon Wong
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