Considerations for Characterizing Protein Expression Changes with SWATH®-MS

Sequential window acquisition of all theoretical mass spectra (SWATH®-MS) can reproducibly and accurately monitor thousands of proteins with high sensitivity in a single run. This data-independent acquisition method has become a powerful technique for quantification. Here, important steps in a typical SWATH®-MS workflow, including sample preparation, data acquisition, spectral libraries, data processing with Skyline, and statistical analyses, are discussed. An example of characterizing protein expression changes using SWATH®-MS is described to illustrate a typical SWATH®-MS workflow.