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 1.0.0

Installation

From Bioconductor: MSstatsTMT

MSstatsTMT 1.4.1 (Bioconductor version : Release 3.10, R version >= 3.6)

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,  Northeastern University
  • Meena Choi,  Northeastern University

Citing MSstatsTMT

  • R package : Huang T, Choi M, Vitek O (2019). MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. R package version 1.4.3, http://msstats.org/msstatstmt/. DOI:10.18129/B9.bioc.MSstatsTMT
  • manuscripts in preparation