| MSstats::MSstats | MSstats: Protein/Peptide significance analysis | HTML | source | R code | |
| MSstats::MSstatsMetabolomics | MSstats: Metabolomics workflow with MZMine | HTML | source | R code | |
| MSstats::MSstatsPlus | MSstats+: Peak quality-weighted differential analysis | HTML | source | R code | |
| MSstats::MSstatsWorkflow | MSstats: End to End Workflow | HTML | source | R code |