MSstats is an R-based/Bioconductor package for statistical relative quantification of peptides and proteins in mass spectrometry-based proteomic experiments. It is applicable to multiple types of sample preparation, including label-free workflows, workflows that use stable isotope labeled reference proteins and peptides, and work-flows that use fractionation. It is applicable to targeted Selected Reactin Monitoring(SRM), Data-Dependent Acquisiton(DDA or shotgun), and Data-Independent Acquisition(DIA or SWATH-MS). This github page is for sharing source and testing. The official webpage is msstats.org