MSstats statistics

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MSstats specifications


Unique identifier OMICS_08556
Name MSstats
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Artistic License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
R, Rcpp, MSnbase, reshape
Maintained Yes


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  • person_outline Meena Choi <>

Publication for MSstats

MSstats in publications

PMCID: 5904110
PMID: 29666374
DOI: 10.1038/s41467-018-03936-z

[…] (nonlinear dynamics). the output of progenesis is a list of quantified spectral features representing peptides of cell surface proteins with multiple charge states and differential modifications. in msstats3 (v3.2.2), the features were log-transformed, and then subjected to constant normalization. protein fold changes and their statistical significance between paired conditions were tested using […]

PMCID: 5893242
PMID: 29662647
DOI: 10.18632/oncotarget.24632

[…] relative to the noninvasive tumor (4 = m5-t2) led to three lists of proteins of interest. these lists gave log2 fold changes in protein content, for which p values < 0.05 were recorded for both msstats and markerview statistical analysis (343 proteins for 1 vs 4, 354 proteins for 2 vs 4, and 350 proteins for 3 vs 4). between these three lists, 137 proteins were shared by the three invasive […]

PMCID: 5885015
PMID: 29557774
DOI: 10.1099/mgen.0.000163

[…] the detection of the protein in both species. the differences in protein fold changes and the corresponding fdr corrections between m. tuberculosis h37rv and m. bovis af2122/97 were calculated using msstats []. a |log2fc|>0.56 and an fdr<0.05 was required for a protein to be defined as differentially expressed between m. tuberculosis h37rv and m. bovis af2122/97., all animal procedures […]

PMCID: 5947139
PMID: 29528492
DOI: 10.1111/nph.15077

[…] was assessed using sweed with the threshold to reject neutrality at the 99th percentile of the neutral clr values. the variation of h norm in the same neutral datasets was assessed using the msstats software ( and the threshold was chosen as the 99.9th percentile to minimize the number of false positives as a result of the likely deviation of barley […]

PMCID: 5844114
PMID: 29541007
DOI: 10.1186/s12014-018-9189-x

[…] with a nano-chip-lc agilent infinity series hplc1290 system. peptides were separated by applying 19┬ámin gradient from 8 to 30% acetonitrile. the statistical analysis of mrm data was performed with msstats (v.2.3.5) []., melanoma cell cultures were established from surplus cerebral melanoma metastases after having obtained written, informed consent approved by the local irb (ek647 and ek800). […]

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MSstats institution(s)
Department of Statistics, Purdue University, West Lafayette, IN, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Computer Science, Purdue University, West Lafayette, IN, USA
MSstats funding source(s)
The work was supported in part by the NSF CAREER award 1054826 and the NSF SI2-SSE award 1047962.

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