MSstats statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Downstream analysis chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

MSstats specifications

Information


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
Requirements
R, Rcpp, MSnbase, reshape
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Meena Choi <>

Publication for MSstats

MSstats in publications

 (60)
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 (https://github.com/molpopgen/msstats) 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). […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

MSstats reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MSstats