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Bioinformatics Advance Access published online on February 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti300
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received December 10, 2004
Revised January 19, 2005
Accepted January 27, 2005

Applications note

SpecAlign - processing and alignment of mass spectra datasets

Jason W. H. Wong 1*, Gerard Cagney 2, and Hugh M. Cartwright 1

1 Chemistry Department, Oxford University, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, ENGLAND
2 Conway Institute, University College Dublin, Belfield, Dublin 4, IRELAND

* To whom correspondence should be addressed.
Jason W. H. Wong, E-mail: jason.wong{at}chem.ox.ac.uk


  Abstract

Summary: Pre-processing of chromatographic profile or mass spectral data is an important aspect of many types of proteomics and biomarker discovery experiments. Here we present a graphical computational tool, SpecAlign, that enables simultaneous visualization and manipulation of multiple datasets. SpecAlign not only provides all common processing functions, but also uniquely implements an algorithm that enables the complete alignment of each mass spectrum within a loaded dataset. We demonstrate its utility by aligning two datasets each containing six spectra, one set was acquired prior to instrument calibration and the other following calibration.

Availability: The software is free of charge and available for download from http://ptcl.chem.ox.ac.uk/~jwong/specalign. Supports Windows operating systems including Windows 9X/NT/2000/XP.


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