MSstatsTMT : Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling.

MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance.

Documentation

User guide for MSstatsTMT 2.0.0 (MSstatsTMT v2 is released)
How to prepare annotation file for using MSstatsTMT

Installation

From Bioconductor: MSstatsTMT

MSstatsTMT 2.2.7 (Bioconductor version : Release 3.14, R version >= 4.1)

Type the following in R console window

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSstatsTMT")
library(MSstatsTMT)

From GitHub: MSstatsTMT

MSstatsTMT Bioconductor Development version : link
The development version of the package MSstats is the most recent and is available here. The versioning of the main package is updated twice a year, to synchronize with the Bioconductor release.

Maintainers

Ting Huang, thuang0703@gmail.com
Mateusz Staniak, mtst@mstaniak.pl

Citing MSstatsTMT

Huang T, Choi M, Tzouros M, Golling S, Pandya N, Banfai B, Dunkley T, Vitek O (2020). “MSstatsTMT: Statistical detection of differentially abundant proteins in experiments with isobaric labeling and multiple mixtures.” Molecular & Cellular Proteomics, 19(10), 1706-1723.

TMT