Something new to test out for the new year #MSDAP was just published. "The #MassSpectrometry Downstream Analysis Pipeline (MS-DAP) is an open-source R package for analyzing and interpreting #label-free #proteomics datasets". It takes output from many upstream search pipelines like #MSFragger, #MetaMorpheous, #DIA-NN, #Spectronaut, #MaxQuant etc. and then applies a range of QC and statistical workflows.
https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00513

https://github.com/ftwkoopmans/msdap