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

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

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