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Bioinformatics Advance Access published online on February 26, 2008
Bioinformatics, 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 1, Navdeep Jaitly 1, Samuel O. Purvine 1, Matthew E. Monroe 1, Kenneth J. Auberry 1, Joshua N. Adkins 1 and Richard D. Smith *,1

1Pacific Northwest National Laboratory, Richland, WA 99354 USA.

*To whom correspondence should be addressed. Dr. Richard D. Smith, E-mail: rds{at}pnl.gov


  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: Prof. Alfonso Valencia

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

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