MSstatsPTM : Tool for detecting differentially abundant PTMs in shotgun mass spectrometry-based proteomic experiments.

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.



MSstatsPTM Label Free Workflow Example
MSstatsPTM TMT Workflow Example


From Bioconductor: MSstatsPTM

MSstatsPTM 1.4.2 (Bioconductor version : Release 3.14, R version >= 4.1)

Type the following in R console window

if (!require("BiocManager", quietly = TRUE))

From GitHub: MSstatsPTM

MSstatsPTM Bioconductor Development version : link
The development version of the package MSstatsPTM 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.