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. 2008 Apr 1;24(7):1021-3.
doi: 10.1093/bioinformatics/btn063. Epub 2008 Feb 26.

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

Anoop M Mayampurath  1 , Navdeep Jaitly, Samuel O Purvine, Matthew E Monroe, Kenneth J Auberry, Joshua N Adkins, Richard D Smith
Affiliations

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

Anoop M Mayampurath et al. Bioinformatics. .

Abstract

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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Figures

Figure 1
Figure 1
Mass Differential (DelM) vs. SEQUEST Xcorr for all hits [left] and filtered hits [right] for a single LTQ_Orbitrap LC-MS/MS dataset. Filters used – DelCn2 >=0.1, Xcorr >= 1.9 for 1+ peptides, Xcorr >=2.2 for 2+ peptides, Xcorr >=3.2 for >= 3+ peptides.
Figure 2
Figure 2
Histogram of DelM values for filtered hits across four Shewanella oneidensis LC-MS/MS datasets
See this image and copyright information in PMC

References

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