Abstract
Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) is an emerging proteomic platform for label free quantification. This platform is based on data independent acquisition (DIA) principle for simultaneous protein identification and quantification. SWATH-MS requires establishment of spectral library which is discussed in this chapter. SWATH-MS data analysis requires targeted data extraction, data normalization. Typical presentation of results from experiments using SWATH-MS is principal component analysis. Several pipelines of DIA analysis are available, however MarkerView and Skyline are two the most commonly used.
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