SWATH2stats

SWATH2stats is an R package to enhance the processing and analysis of SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra) data, a targeted proteomics technique enabling the measurement of numerous proteins with high reproducibility. While OpenSWATH is widely used for peptide identification and quantification in SWATH-MS data, downstream statistical tools like MSstats, mapDIA, and aLFQ face challenges in data transfer from OpenSWATH. SWATH2stats addresses this issue by facilitating data conversion into a format directly readable by downstream tools. The package offers additional functionalities such as annotation, variation and reproducibility analysis, false discovery rate (FDR) estimation, and advanced filtering.