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Open Access Highly Accessed Software

Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing

Andreas M Boehm1, Robert P Galvin2 and Albert Sickmann1*

Author Affiliations

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

2 Applied Biosystems, Applera UK, Lingley House, 120 Birchwood Boulevard, Warrington, Cheshire, WA3 7QH, UK

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BMC Bioinformatics 2004, 5:162  doi:10.1186/1471-2105-5-162

Published: 26 October 2004

Abstract

Background

Mass spectrometry based proteomics result in huge amounts of data that has to be processed in real time in order to efficiently feed identification algorithms and to easily integrate in automated environments. We present wiff2dta, a tool created to convert MS/MS data obtained using Applied Biosystem's QStar and QTrap 2000 and 4000 series.

Results

Comparing the performance of wiff2dta with the standard tools, we find wiff2dta being the fastest solution for extracting spectrum data from ABIs raw file format. wiff2dta is at least 10% faster than the standard tools. It is also capable of batch processing and can be easily integrated in high throughput environments. The program is freely available via http://www.protein-ms.de webcite, http://sourceforge.net/projects/protms/ webcite and is also available from Applied Biosystems.

Conclusions

wiff2dta offers the possibility to run as stand-alone application or within a batch process as command-line tool integrated in automation and high-throughput environments. It is more efficient than the state-of-the-art tools provided.