We present a flexible, user-friendly R package called protti for comprehensive quality control, analysis and interpretation of quantitative bottom-up proteomics data. protti supports the analysis of protein-centric data such as those associated with protein expression analyses, as well as peptide-centric data such as those resulting from limited proteolysis-coupled mass spectrometry analysis. Due to its flexible design, it supports analysis of label-free, data-dependent, data-independent and targeted proteomics datasets. protti can be run on the output of any search engine and software package commonly used for bottom-up proteomics experiments such as Spectronaut, Skyline, MaxQuant or Proteome Discoverer, adequately exported to table format.