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MSQuant specifications


Unique identifier OMICS_02487
Name MSQuant
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Stability Stable
Maintained Yes


No version available

Publication for MSQuant

MSQuant citations


Membrane potential independent transport of NH3 in the absence of ammonium permeases in Saccharomyces cerevisiae

BMC Syst Biol
PMCID: 5392931
PMID: 28412970
DOI: 10.1186/s12918-016-0381-1
call_split See protocol

[…] ptides with Mascot score <10 were removed and only the highest scoring peptide matches for each query listed under the highest scoring protein (bold red) were selected. Proteins were quantified using MSQuant version 2.0b7 [] by importing the Mascot results html file with the corresponding raw mass spectrometric data files. MSQuant automatically calculated peptide and protein ratios by using a 13C […]


Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells

PLoS Comput Biol
PMCID: 5376343
PMID: 28306714
DOI: 10.1371/journal.pcbi.1005432

[…] Quantification was done on at least two MS spectra per protein by using MSQuant v1.4.1 software developed by Mann and colleagues [] ( Data were manually inspected and corrected when necessary. […]


PTB and TIAR binding to insulin mRNA 3′ and 5′UTRs; implications for insulin biosynthesis and messenger stability

PMCID: 5035359
PMID: 27699280
DOI: 10.1016/j.heliyon.2016.e00159
call_split See protocol

[…] yme specificity as well as the instrument settings were kept unchanged. Parsing of data and statistical analysis of the search results reported by Mascot were performed using the open-source software MSQuant . […]


Biochemical and cellular characterization of transcription factors binding to the hyperconserved core promoter associated M4 motif

BMC Genomics
PMCID: 5006282
PMID: 27576892
DOI: 10.1186/s12864-016-3033-3
call_split See protocol

[…] The raw Orbitrap MS files were processed with MSQuant v2.0b5 and MaxQuant v1.0.12.31 [, ] two powerful computational platform for SILAC based quantitative proteomics, using the following settings: Enzyme specificity was set to trypsin, allowing t […]


A phospho dependent mechanism involving NCoR and KMT2D controls a permissive chromatin state at Notch target genes

Nucleic Acids Res
PMCID: 4889922
PMID: 26912830
DOI: 10.1093/nar/gkw105

[…] e 500 or 1000 counts for MS2 depending on the experiment. An activation q = 0.25 and activation time of 30 ms was applied.Raw files were processed into peak lists by DTASuperCharge 2.0b1 [part of the MSQuant 2.0b7 software environment ()] and searched with Mascot 2.2 against the human International Protein Index protein database (IPI, version 3.65) combined with frequently observed contaminants an […]


IL 1α is a DNA damage sensor linking genotoxic stress signaling to sterile inflammation and innate immunity

Sci Rep
PMCID: 4593953
PMID: 26439902
DOI: 10.1038/srep14756

[…] e eluted with a linear gradient of 10–60% buffer B (80% ACN and 0.5% acetic acid) at a flow rate of 250 nL/min over 60 min. MS data were processed into peak lists by DTASuperCharge 2.0b1 (part of the MSQuant 2.0b7 software environment) and searched with Mascot 2.2 against the mouse International Protein Index protein database (IPI, version 3.68) combined with frequently observed contaminants and c […]


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MSQuant institution(s)
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Center for Experimental Bioinformatics, Odense, Denmark

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