Package: MSstats 4.21.0

Meena Choi

MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.

Authors:Meena Choi [aut, cre], Mateusz Staniak [aut], Devon Kohler [aut], Tony Wu [aut], Deril Raju [aut], Tsung-Heng Tsai [aut], Ting Huang [aut], Olga Vitek [aut]

MSstats_4.21.0.tar.gz
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MSstats_4.21.0.tgz(r-4.6-x86_64)MSstats_4.21.0.tgz(r-4.6-arm64)MSstats_4.19.2.tgz(r-4.5-x86_64)MSstats_4.19.2.tgz(r-4.5-arm64)
MSstats_4.21.0.tar.gz(r-4.7-arm64)MSstats_4.21.0.tar.gz(r-4.7-x86_64)MSstats_4.21.0.tar.gz(r-4.6-arm64)MSstats_4.21.0.tar.gz(r-4.6-x86_64)
MSstats_4.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MSstats/json (API)

# Install 'MSstats' in R:

install.packages('MSstats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

DDARawData - Example dataset from a label-free DDA, a controlled spike-in experiment.
DDARawData.Skyline - Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.
DIARawData - Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.
example_SDRF - Example SDRF.
SRMRawData - Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study

On BioConductor:MSstats-4.21.0(bioc 3.24)MSstats-4.20.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology massspectrometry proteomics software normalization qualitycontrol timecourse openblas cpp

9.41 score 7 packages 383 scripts 1.3k downloads 115 mentions 45 exports 92 dependencies

Last updated from:a186133bc9. Checks:1 ERROR, 8 WARNING, 2 OK, 3 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	189
linux-devel-arm64	WARNING	253
linux-devel-x86_64	WARNING	282
source / vignettes	OK	338
linux-release-arm64	WARNING	248
linux-release-x86_64	WARNING	354
macos-release-arm64	WARNING	139
macos-release-x86_64	WARNING	472
macos-oldrel-arm64	FAIL	74
macos-oldrel-x86_64	FAIL	179
windows-devel	WARNING	224
windows-release	WARNING	240
windows-oldrel	FAIL	73
wasm-release	OK	164

Exports:checkRepeatedDesign dataProcess dataProcessPlots designSampleSize designSampleSizePlots DIANNtoMSstatsFormat DIAUmpiretoMSstatsFormat extractSDRF FragPipetoMSstatsFormat getProcessed getSamplesInfo getSelectedProteins groupComparison groupComparisonPlots groupComparisonQCPlots makePeptidesDictionary MaxQtoMSstatsFormat modelBasedQCPlots MSstatsContrastMatrix MSstatsGroupComparison MSstatsGroupComparisonOutput MSstatsGroupComparisonSingleProtein MSstatsHandleMissing MSstatsMergeFractions MSstatsNormalize MSstatsPrepareForDataProcess MSstatsPrepareForGroupComparison MSstatsPrepareForSummarization MSstatsQualityMetricsPlot MSstatsSelectFeatures MSstatsSummarizationOutput MSstatsSummarizeSingleLinear MSstatsSummarizeSingleTMP MSstatsSummarizeWithSingleCore OpenMStoMSstatsFormat OpenSWATHtoMSstatsFormat PDtoMSstatsFormat ProgenesistoMSstatsFormat quantification savePlot SDRFtoAnnotation SkylinetoMSstatsFormat SpectronauttoMSstatsFormat theme_msstats validateAnnotation

Dependencies:askpass backports base64enc bitops boot bslib cachem caTools checkmate cli cpp11 crosstalk curl data.table digest dplyr evaluate farver fastmap fontawesome fs generics ggplot2 ggrepel glue gplots gtable gtools highr htmltools htmlwidgets httr isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle limma lme4 log4r magrittr marray MASS Matrix memoise mime minqa MSstatsConvert nlme nloptr openssl otel pillar pkgconfig plotly preprocessCore promises purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown S7 sass scales statmod stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

MSstats: End to End Workflow

Rendered fromMSstatsWorkflow.Rmdusingknitr::knitron May 28 2026.

Last update: 2025-03-12
Started: 2024-10-15

MSstats: Protein/Peptide significance analysis

Rendered fromMSstats.Rmdusingknitr::knitron May 28 2026.

Last update: 2023-07-28
Started: 2015-10-01

MSstats+: Peak quality-weighted differential analysis

Rendered fromMSstatsPlus.Rmdusingknitr::knitron May 28 2026.

Last update: 2026-01-22
Started: 2025-09-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check if data represents repeated measurements design	checkRepeatedDesign
Process MS data: clean, normalize and summarize before differential analysis	dataProcess
Visualization for explanatory data analysis	dataProcessPlots
Example dataset from a label-free DDA, a controlled spike-in experiment.	DDARawData
Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.	DDARawData.Skyline
Planning future experimental designs of Selected Reaction Monitoring (SRM), Data-Dependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA or SWATH-MS) experiments in sample size calculation	designSampleSize
Visualization for sample size calculation	designSampleSizePlots
Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.	DIARawData
Example SDRF.	example_SDRF
Extract experimental design from MSstats format into SDRF format	extractSDRF
Get feature-level data to be used in the MSstatsSummarizationOutput function	getProcessed
Get information about number of measurements for each group	getSamplesInfo
Get proteins based on names or integer IDs	getSelectedProteins
Whole plot testing	groupComparison
Visualization for model-based analysis and summarizing differentially abundant proteins	groupComparisonPlots
Visualization for model-based quality control in fitting model	groupComparisonQCPlots
Prepare a peptides dictionary for global standards normalization	makePeptidesDictionary
Visualization for model-based quality control in fitting model	modelBasedQCPlots
Create a contrast matrix for groupComparison function	MSstatsContrastMatrix
Group comparison	MSstatsGroupComparison
Create output of group comparison based on results for individual proteins	MSstatsGroupComparisonOutput
Group comparison for a single protein	MSstatsGroupComparisonSingleProtein
Handle censored missing values	MSstatsHandleMissing
Re-format the data before feature selection	MSstatsMergeFractions
Normalize MS data	MSstatsNormalize
Prepare data for processing by `dataProcess` function	MSstatsPrepareForDataProcess
Prepare output for dataProcess for group comparison	MSstatsPrepareForGroupComparison
Prepare feature-level data for protein-level summarization	MSstatsPrepareForSummarization
Plot quality metrics from converter output	MSstatsQualityMetricsPlot
Feature selection before feature-level data summarization	MSstatsSelectFeatures
Post-processing output from MSstats summarization	MSstatsSummarizationOutput
Linear model-based summarization for a single protein	MSstatsSummarizeSingleLinear
Tukey Median Polish summarization for a single protein	MSstatsSummarizeSingleTMP
Feature-level data summarization with multiple cores	MSstatsSummarizeWithMultipleCores
Feature-level data summarization with 1 core	MSstatsSummarizeWithSingleCore
Protein sample quantification or group quantification	quantification
Save a plot to pdf file	savePlot
Convert SDRF experimental design file into an MSstats annotation file	SDRFtoAnnotation
Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study	SRMRawData
Theme for MSstats plots	theme_msstats
Check if annotation matches intended experimental design	validateAnnotation