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MS-Deconv specifications


Unique identifier OMICS_04042
Name MS-Deconv
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Advanced
Version 0.8
Stability Stable
Maintained Yes




No version available



  • person_outline Pavel Pevzner

Publication for MS-Deconv

MS-Deconv citations


It is time for top down venomics

PMCID: 5648493
PMID: 29075288
DOI: 10.1186/s40409-017-0135-6

[…] st and confident automated processing of high resolution MS1 and MS2 data. The complex data obtained need to be deconvoluted to simplify the protein identification process and the softwares TRASH and MS-Deconv are commonly used [, ]. ProSight PTM was the first tool developed and further improved for a complete automated search using robust scores and statistics parameters to enable the identificat […]


Biochemical, Transcriptomic and Proteomic Analyses of Digestion in the Scorpion Tityus serrulatus: Insights into Function and Evolution of Digestion in an Ancient Arthropod

PLoS One
PMCID: 4398375
PMID: 25875018
DOI: 10.1371/journal.pone.0123841

[…] -Orbitrap Velos (Thermo Fisher) as previously described []. The raw LC-MS/MS data files were processed into peak lists using the software ReAdW 4.3.1. Mass spectra were deconvoluted using the program MS-deconv []. The files generated from MS-deconv were then analyzed by MASCOT (Matrix Sciences), an error tolerance of 0.05 Da was allowed only in the parent ion and also one miss cleavage site by try […]


A new scoring function for top down spectral deconvolution

BMC Genomics
PMCID: 4378558
PMID: 25523396
DOI: 10.1186/1471-2164-15-1140
call_split See protocol

[…] nally, the intensities of the theoretical peaks are initialized as their probabilities and further scaled based on the intensities of the matched experimental peaks (Figure ). Following the method in MS-Deconv, we scale theoretical peak intensities so that the sum of the intensities of the top three theoretical peaks equals that of their corresponding experimental peaks. If the scaled intensity of […]


Effective Protein Separation by Coupling Hydrophobic Interaction and Reverse Phase Chromatography for Top down Proteomics

Anal Chem
PMCID: 4144745
PMID: 24968279
DOI: 10.1021/ac501836k
call_split See protocol

[…] Raw top two data-dependent MS data collected by Xcalibur were first processed with MS-Deconv, a combinatorial algorithm for reliable isotopic distribution deconvolution and charge state assignment for all the observed ions to generate MSAlign files containing monoisotopic mass, inte […]


Top down Proteomics Reveals Concerted Reductions in Myofilament and Z disc Protein Phosphorylation after Acute Myocardial Infarction*

PMCID: 4189000
PMID: 24969035
DOI: 10.1074/mcp.M114.040675
call_split See protocol

[…] The raw MS/MS data were converted to mzXML files and deconvoluted with MS-Deconv (release version 0.8.0) (), a combinatorial algorithm that determines the monoisotopic mass and charge for all of the fragment ions present in an MS/MS spectrum. Subsequently, to identify th […]


Capillary Zone Electrophoresis–Electrospray Ionization Tandem Mass Spectrometry for Top Down Characterization of the Mycobacterium marinum Secretome

Anal Chem
PMCID: 4033641
PMID: 24725189
DOI: 10.1021/ac500092q
call_split See protocol

[…] The tandem spectra were decharged and deisotoped by MS-Deconv (version, followed by database searching with MS-Align+ software (version Raw files from Q Exactive were first converted to mzXML files with ReAdW (version 4.3.1). T […]

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MS-Deconv institution(s)
Pharmacology, Chemistry and Biochemistry, University of California, San Diego, CA, USA; Department of Chemistry and Biochemistry, University of Maryland, College Park, MA, USA; Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, USA; Pasarow Mass Spectrometry Laboratory, Neuropysychiatric Institute-Semel Institute, University of California, Los Angeles, CA, USA
MS-Deconv funding source(s)
This work was supported by National Institutes of Health Grant P-41-RR024851 from the National Center for Research Resources.

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