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.
From Bioconductor: MSstatsTMT
MSstatsTMT 2.0.0 (Bioconductor version : Release 3.13, 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.
- 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.