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Bioinformatics Advance Access originally published online on February 26, 2008
Bioinformatics 2008 24(7):1021-1023; doi:10.1093/bioinformatics/btn063
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

Anoop M. Mayampurath , Navdeep Jaitly , Samuel O. Purvine , Matthew E. Monroe , Kenneth J. Auberry , Joshua N. Adkins and Richard D. Smith *

Pacific Northwest National Laboratory, Richland, WA 99354, USA

*To whom correspondence should be addressed.


  Abstract

Summary: DeconMSn accurately determines the monoisotopic mass and charge state of parent ions from high-resolution tandem mass spectrometry data, offering significant improvement for LTQ_FT and LTQ_Orbitrap instruments over the commercially delivered Thermo Fisher Scientific's extract_msn tool. Optimal parent ion mass tolerance values can be determined using accurate mass information, thus improving peptide identifications for high-mass measurement accuracy experiments. For low-resolution data from LCQ and LTQ instruments, DeconMSn incorporates a support-vector-machine-based charge detection algorithm that identifies the most likely charge of a parent species through peak characteristics of its fragmentation pattern.

Availability: http://ncrr.pnl.gov/software/ or http://www.proteomicsresource.org/

Contact: rds{at}pnl.gov

Supplementary information: PowerPoint presentation/Poster on http://ncrr.pnl.gov/software/.

Associate Editor: Alfonso Valencia

Received on September 30, 2007; revised on February 8, 2008; accepted on February 16, 2008

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