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Bioinformatics Advance Access published online on May 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth328
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 4, 2004
Revised May 10, 2004
Accepted May 10, 2004

Applications note

Command line tool for calculating theoretical ms spectra for given sequences

Andreas M. Boehm 1, Florian Grosse-Coosmann 1, Albert Sickmann 1*

1 Protein Mass Spectrometry and Functional Proteomics Group, Rudolf-Virchow-Center for Experimental Biomedicine, Universitaet Wuerzburg, Versbacher Strasse 9, D-97078 Wuerzburg, Germany

* To whom correspondence should be addressed. E-mail: albert.sickmann{at}virchow.uni-wuerzburg.de.


  Abstract

Summary: Scientists usually want to verify the ion matching process of algorithms that look up peptide sequences in DNA or protein databases. The verification step is often done numerically or visually. Not all search algorithms present the appropriate theoretical spectrum information within their results. Thus, the theoretical spectrum for each result should be calculated from the sequence of the matched peptide. We present an operating-system-independent command line tool for this purpose that can be integrated easily into complex as well as existing environments, and can be used to present the theoretical spectrum to the user in either graphical or tabular format by third party products.

Availability: The code is available via the website http://www.protein-ms.de.


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