Here we present PBLMM, a standalone desktop application for differential expression analysis of proteomics data, together with a python package that allows streamlined data analysis workflows implementing the PBLMM algorithm. PBLMM is easy to use without scripting experience and calculates differential expression by peptide based linear mixed regression models. The application and the python packages are freely available under the GNU GPLv3 license:

PBLMM desktop application
mssuite python package