SWATH: A data-independent tandem mass spectrometry method to quantify C enrichment in cellular metabolites and fragments

Recently, the sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) method coupled with liquid chromatography has been demonstrated for the quantification of isotopic C enrichment in a large number of cellular metabolites and fragments. SWATH, a data–independent acquisition (DIA) method, alleviates the need for data deconvolution and shows greater accuracy in the quantification of low abundance isotopologs of fragments thereby resulting in a lower systematic error. Here we provide a detailed protocol for the design of Q1 mass isolation windows and the post–acquisition data analysis with emphasis on the untargeted nature of SWATH.