The einprot package contains a set of workflows for statistical analysis of quantitative proteomics data processed with MaxQuant (LFQ), FragPipe (LFQ) or Proteome Discoverer (TMT-labelled).


You can install the development version of einprot from GitHub with:



For more details about how to use einprot, we refer to the vignette.

A collection of example reports generated by applying einprot to a variety of public data sets is available here.


If you are using einprot, please cite

Soneson C, Iesmantavicius V, Hess D, Stadler MB, Seebacher J (2023). einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data. Journal of Open Source Software, 8(89), 5750.

Need help?

If you run into problems when using einprot, please first check whether the answer is available in the help pages for the individual functions or in the vignette. If not, please open an issue and explain your problem. Try to provide a reproducible example, and always include the code you used, that will make it much easier for us to help.


If you would like to contribute to einprot, you can do so by sending a pull request to this repository. If the contribution involves changes in the functionality provided by einprot, we encourage you to first open an issue to discuss the intended contribution.