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Bioinformatics Advance Access originally published online on November 22, 2006
Bioinformatics 2007 23(2):264-265; 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

PrepMS: TOF MS data graphical preprocessing tool

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

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

*To whom correspondence should be addressed.


  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, if desired, can be changed by the user. 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

Contact: ykarpi{at}mdanderson.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Limsoon Wong

Received on October 10, 2006; accepted on November 15, 2006

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