Metaprotr is an R package that contains a set of tools for descriptive analysis of metaproteomics data generated from high-throughput mass spectrometry instruments. These tools allow to cluster peptides and proteins abundance, expressed as spectral counts, and to manipulate them in groups of metaproteins. This information can be represented using multiple visualization functions to portray the global metaproteome landscape and to differentiate samples or conditions, in terms of abundance of metaproteins, taxonomic levels and/or functional annotation. The provided tools allow to implement flexible analytical pipelines that can be easily applied to studies interested in metaproteomics analysis.

Download and install

Metaprotr can be obtained from the CRAN repository. In an R session, it can be installed by typing:


Source files are also available in the ForgeMIA repository. Download the tar.gz file and install the package in an R session:

install.packages("~/your/directory/metaprotr-v.1.2.2.tar.gz", repos = NULL, type = "source")


The package documentation and the cheatsheet describes the usage of the different functions. In addition, a curated script is also available showing the application of metaprotr to analyzethe metaproteomes from intestinal microbiota.


Metaprotr is a free software distributed under the terms of the GNU GENERAL PUBLIC licence v3.


The source code of metaprotr is hosted in ForgeMIA. The development is open and free, you are welcome to contribute, copy, modify, fork if you need it and/or send bug reports by respecting the terms of the licence.