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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manual.pdf |manual.html✨
DESCRIPTION
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.

immunooncologymassspectrometryproteomicssoftwarenormalizationqualitycontroltimecourseopenblascpp

9.33 score 7 packages 383 scripts 1.3k downloads 115 mentions 45 exports 91 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksERROR206
linux-devel-arm64WARNING212
linux-devel-x86_64WARNING334
source / vignettesOK302
linux-release-arm64WARNING222
linux-release-x86_64WARNING330
macos-release-arm64WARNING153
macos-release-x86_64WARNING316
macos-oldrel-arm64FAIL75
macos-oldrel-x86_64FAIL165
windows-devel-x86_64WARNING265
windows-release-x86_64WARNING246
windows-oldrel-x86_64FAIL108
wasm-releaseOK180

Exports:checkRepeatedDesigndataProcessdataProcessPlotsdesignSampleSizedesignSampleSizePlotsDIANNtoMSstatsFormatDIAUmpiretoMSstatsFormatextractSDRFFragPipetoMSstatsFormatgetProcessedgetSamplesInfogetSelectedProteinsgroupComparisongroupComparisonPlotsgroupComparisonQCPlotsmakePeptidesDictionaryMaxQtoMSstatsFormatmodelBasedQCPlotsMSstatsContrastMatrixMSstatsGroupComparisonMSstatsGroupComparisonOutputMSstatsGroupComparisonSingleProteinMSstatsHandleMissingMSstatsMergeFractionsMSstatsNormalizeMSstatsPrepareForDataProcessMSstatsPrepareForGroupComparisonMSstatsPrepareForSummarizationMSstatsQualityMetricsPlotMSstatsSelectFeaturesMSstatsSummarizationOutputMSstatsSummarizeSingleLinearMSstatsSummarizeSingleTMPMSstatsSummarizeWithSingleCoreOpenMStoMSstatsFormatOpenSWATHtoMSstatsFormatPDtoMSstatsFormatProgenesistoMSstatsFormatquantificationsavePlotSDRFtoAnnotationSkylinetoMSstatsFormatSpectronauttoMSstatsFormattheme_msstatsvalidateAnnotation

Dependencies:askpassbackportsbase64encbitopsbootbslibcachemcaToolscheckmateclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2ggrepelgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmalme4magrittrmarrayMASSMatrixmemoisemimeminqaMSstatsConvertnlmenloptropensslotelpillarpkgconfigplotlypreprocessCorepromisespurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownS7sassscalesstatmodstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

MSstats+: Peak quality-weighted differential analysis
Load packages | Converter | Load data | Run converter | Check model fit | Manual formatting and data conversion | Data processing and summarization | Differential analysis | Compare results to base MSstats | MSstatsBig
Rendered fromMSstatsPlus.Rmdusingknitr::knitr

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

MSstats: End to End Workflow
MSstats: Protein/Peptide significance analysis | Introduction | Installation | 1. Workflow | 1.1 Raw Data | 1.2 Loading PD Data to MSstats | 1.3 Converters | 1.4 Data Process | 1.4.1 Data Processing Options | Normalization | Feature Selection | Missing Value Imputation | 1.4.2 Data Process Plots | __1.5 Modeling __ | 1.5.1 How to Account for Covariates | Step 1: Set up your conditions | Step 2: Create a contrast matrix | 1.5.2 groupComparisonPlot | 1.6 GroupComparisonQCPlots | 1.7 Sample Size Calculation | 1.7.1 Sample Size Calculation Plot | 1.8 Quantification from groupComparison Data
Rendered fromMSstatsWorkflow.Rmdusingknitr::knitr

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

MSstats: Protein/Peptide significance analysis
SkylinetoMSstatsFormat | Arguments | Example | MaxQtoMSstatsFormat | ProgenesistoMSstatsFormat | SpectronauttoMSstatsFormat | dataProcess | Details of outputs | RunlevelData from dataProcess | ComparisonResult from groupComparison : one or two columns will be added. | dataProcessPlots | groupComparison | groupComparisonPlots | modelBasedQCPlots | designSampleSize | designSampleSizePlots | quantification
Rendered fromMSstats.Rmdusingknitr::knitr

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

Readme and manuals

Help Manual

Help pageTopics
Check if data represents repeated measurements designcheckRepeatedDesign
Process MS data: clean, normalize and summarize before differential analysisdataProcess
Visualization for explanatory data analysisdataProcessPlots
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 calculationdesignSampleSize
Visualization for sample size calculationdesignSampleSizePlots
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 formatextractSDRF
Get feature-level data to be used in the MSstatsSummarizationOutput functiongetProcessed
Get information about number of measurements for each groupgetSamplesInfo
Get proteins based on names or integer IDsgetSelectedProteins
Whole plot testinggroupComparison
Visualization for model-based analysis and summarizing differentially abundant proteinsgroupComparisonPlots
Visualization for model-based quality control in fitting modelgroupComparisonQCPlots
Prepare a peptides dictionary for global standards normalizationmakePeptidesDictionary
Visualization for model-based quality control in fitting modelmodelBasedQCPlots
Create a contrast matrix for groupComparison functionMSstatsContrastMatrix
Group comparisonMSstatsGroupComparison
Create output of group comparison based on results for individual proteinsMSstatsGroupComparisonOutput
Group comparison for a single proteinMSstatsGroupComparisonSingleProtein
Handle censored missing valuesMSstatsHandleMissing
Re-format the data before feature selectionMSstatsMergeFractions
Normalize MS dataMSstatsNormalize
Prepare data for processing by `dataProcess` functionMSstatsPrepareForDataProcess
Prepare output for dataProcess for group comparisonMSstatsPrepareForGroupComparison
Prepare feature-level data for protein-level summarizationMSstatsPrepareForSummarization
Plot quality metrics from converter outputMSstatsQualityMetricsPlot
Feature selection before feature-level data summarizationMSstatsSelectFeatures
Post-processing output from MSstats summarizationMSstatsSummarizationOutput
Linear model-based summarization for a single proteinMSstatsSummarizeSingleLinear
Tukey Median Polish summarization for a single proteinMSstatsSummarizeSingleTMP
Feature-level data summarization with multiple coresMSstatsSummarizeWithMultipleCores
Feature-level data summarization with 1 coreMSstatsSummarizeWithSingleCore
Protein sample quantification or group quantificationquantification
Save a plot to pdf filesavePlot
Convert SDRF experimental design file into an MSstats annotation fileSDRFtoAnnotation
Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast studySRMRawData
Theme for MSstats plotstheme_msstats
Check if annotation matches intended experimental designvalidateAnnotation