SWATH-MS is an alternative data-independent acquisition technique in mass spectrometry that allows the collection and storage of the fragmentation spectra of virtually all peptides in a sample. In the process, preselected isolation mass windows are specified and fragmentation of all precursor ion species contained is performed in an efficient, unbiased manner, independent of their abundance. This results in co-fragmentation of simultaneously eluting and close isobaric ion species and generates highly complex MS/MS spectra, which need to be deconvoluted by peptide-centric data analysis approaches. In a peptide-centric analysis, a spectral ion library, also referred to as a SWATH or assay library, is used to extract ion chromatograms in a targeted manner using DIA tools such as OpenSWATH, PeakView or Spectronaut. Comprehensive, high-quality assay libraries support the identification and the consistent and accurate quantification of thousands of peptides representing large fractions of the proteome.