DOI: 10.18129/B9.bioc.MSstatsTMT  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MSstatsTMT.

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

Bioconductor version: 3.17

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.

Author: Ting Huang [aut, cre], Meena Choi [aut], Mateusz Staniak [aut], Sicheng Hao [aut], Olga Vitek [aut]

Maintainer: Ting Huang <thuang0703 at>

Citation (from within R, enter citation("MSstatsTMT")):


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biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 2.8.0
In Bioconductor since BioC 3.8 (R-3.5) (5 years)
License Artistic-2.0
Depends R (>= 4.2)
Imports limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate
Suggests BiocStyle, knitr, rmarkdown, testthat
Depends On Me
Imports Me MSstatsPTM, MSstatsShiny
Suggests Me
Links To Me
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