Package: MSstatsTMT 2.21.0

Devon Kohler

MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.

Authors:Devon Kohler [aut, cre], Ting Huang [aut], Meena Choi [aut], Mateusz Staniak [aut], Tony Wu [aut], Deril Raju [aut], Sicheng Hao [aut], Olga Vitek [aut]

MSstatsTMT_2.21.0.tar.gz
MSstatsTMT_2.21.0.zip(r-4.7)MSstatsTMT_2.21.0.zip(r-4.6)MSstatsTMT_2.21.0.zip(r-4.5)
MSstatsTMT_2.21.0.tgz(r-4.6-any)MSstatsTMT_2.21.0.tgz(r-4.5-any)
MSstatsTMT_2.21.0.tar.gz(r-4.7-any)MSstatsTMT_2.21.0.tar.gz(r-4.6-any)
MSstatsTMT_2.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MSstatsTMT/json (API)
NEWS

# Install 'MSstatsTMT' in R:
install.packages('MSstatsTMT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • annotation.mine - Example of annotation file for raw.mine, which is the output of SpectroMine.
  • annotation.mq - Example of annotation file for evidence, which is the output of MaxQuant.
  • annotation.pd - Example of annotation file for raw.pd, which is the PSM output of Proteome Discoverer
  • evidence - Example of output from MaxQuant for TMT-10plex experiments.
  • input.pd - Example of output from PDtoMSstatsTMTFormat function
  • proteinGroups - Example of proteinGroups file from MaxQuant for TMT-10plex experiments.
  • raw.mine - Example of output from SpectroMine for TMT-6plex experiments.
  • raw.om - Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.
  • raw.pd - Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.

On BioConductor:MSstatsTMT-2.21.0(bioc 3.24)MSstatsTMT-2.20.0(bioc 3.23)

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

immunooncologymassspectrometryproteomicssoftware

6.42 score 3 packages 59 scripts 708 downloads 5 mentions 9 exports 95 dependencies

Last updated from:1dff091661. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

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Exports:dataProcessPlotsTMTdesignSampleSizeTMTgroupComparisonTMTMaxQtoMSstatsTMTFormatOpenMStoMSstatsTMTFormatPDtoMSstatsTMTFormatPhilosophertoMSstatsTMTFormatproteinSummarizationSpectroMinetoMSstatsTMTFormat

Dependencies:askpassbackportsbase64encbitopsbootbslibcachemcaToolscheckmateclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2ggrepelgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmalme4lmerTestlog4rmagrittrmarrayMASSMatrixmemoisemimeminqaMSstatsMSstatsConvertnlmenloptrnumDerivopensslotelpillarpkgconfigplotlypreprocessCorepromisespurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownS7sassscalesstatmodstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

MSstatsTMT : A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Ting Huang ([email protected]), Meena Choi ([email protected]), Mateusz Staniak ([email protected]), Sicheng Hao ([email protected]), Olga Vitek([email protected])

Rendered fromMSstatsTMT.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2022-02-18
Started: 2017-12-13

Readme and manuals

Help Manual

Help pageTopics
Example of annotation file for raw.mine, which is the output of SpectroMine.annotation.mine
Example of annotation file for evidence, which is the output of MaxQuant.annotation.mq
Example of annotation file for raw.pd, which is the PSM output of Proteome Discovererannotation.pd
Visualization for explanatory data analysis - TMT experimentdataProcessPlotsTMT
Planning future experimental designs of Tandem Mass Tag (TMT) experiments acquired with Data-Dependent Acquisition (DDA or shotgun)designSampleSizeTMT
Example of output from MaxQuant for TMT-10plex experiments.evidence
Finding differentially abundant proteins across conditions in TMT experimentgroupComparisonTMT
Example of output from PDtoMSstatsTMTFormat functioninput.pd
Generate MSstatsTMT required input format from MaxQuant outputMaxQtoMSstatsTMTFormat
MSstatsTMT: A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labelingMSstatsTMT-package MSstatsTMT
Generate MSstatsTMT required input format for OpenMS outputOpenMStoMSstatsTMTFormat
Convert Proteome Discoverer output to MSstatsTMT format.PDtoMSstatsTMTFormat
Convert Philosopher (Fragpipe) output to MSstatsTMT format.PhilosophertoMSstatsTMTFormat
Example of proteinGroups file from MaxQuant for TMT-10plex experiments.proteinGroups
Summarizing peptide level quantification to protein level quantificationproteinSummarization
Example of output from SpectroMine for TMT-6plex experiments.raw.mine
Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.raw.om
Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.raw.pd
Import data from SpectroMineSpectroMinetoMSstatsTMTFormat