Registration Open for Bioc2024 July 24-26


This is the development version of MSstatsPTM; for the stable release version, see MSstatsPTM.

Statistical Characterization of Post-translational Modifications

Bioconductor version: Development (3.20)

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, 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.

Author: Devon Kohler [aut, cre], Tsung-Heng Tsai [aut], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

MSstatsPTM LabelFree Workflow HTML R Script
MSstatsPTM TMT Workflow HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version 2.7.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.3)
Imports dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel
System Requirements
Bug Reports
See More
Suggests knitr, rmarkdown, tinytest, covr
Linking To Rcpp
Depends On Me
Imports Me MSstatsLiP, MSstatsShiny
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MSstatsPTM_2.7.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) MSstatsPTM_2.7.0.tgz
macOS Binary (arm64) MSstatsPTM_2.7.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats