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Updated: Jul 7, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
Anoop M Mayampurath1, Navdeep Jaitly, Samuel O Purvine
1Pacific Northwest National Laboratory, Richland, WA 99354, USA.
Unlabelled:
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/.
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