SWATH Proteomics

SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra), a variation of the data-independent acquisition (DIA) approach, allows for great quantitative precision and consistency while analyzing peptides up to 9000 proteins. The main premise is that ions are chosen depending on the electric field differences between quadrupoles. The first quadrupole Q1 chooses ions with a specific mass/charge ratio, while the second quadrupole Q2 works as a collision chamber, causing fragmentation reactions, before scanning the debris ions in a TOF. A single analysis can perform complete identification and quantitative analysis (MS/MSALL) of practically all detected chemicals in the sample. In quantitation analysis, SWATH has a high accuracy and dynamic range. Unlike traditional mass spectrometry quantitative methods, the SWATH technology-based quantitative method directly constructs the XIC of secondary fragment ions, and every point on the curve has sufficient mass spectrometry evidence, increasing quantitative accuracy and reproducibility significantly.