SWATHMS

SWATH-MS, or Sequential Window Acquisition of All Theoretical fragment ion Mass Spectra, is a data-independent acquisition (DIA) mass spectrometry method used primarily in quantitative proteomics. In SWATH-MS, the instrument cycles through a predefined set of isolation windows across a chosen mass-to-charge (m/z) range. Within each window, all precursor ions are fragmented, and their fragment ions are recorded. The result is comprehensive MS/MS data that covers all detectable peptides within the selected m/z range, enabling post-acquisition analysis to identify and quantify proteins across samples.

A typical SWATH-MS workflow relies on a spectral library generated from prior data-dependent acquisition experiments or synthetic standards. SWATH data are then interrogated against this library: peptides are identified by matching observed fragment ion patterns to library spectra, and quantitative information is extracted from fragment ion chromatograms. This approach allows consistent quantification across large sample sets and reduces missing values compared with traditional data-dependent methods.

Advantages of SWATH-MS include broad and reproducible proteome coverage, improved quantitative consistency across multiple samples, and suitability for high-throughput workflows. Limitations involve the dependence on a high-quality spectral library, potential complexity from overlapping fragment spectra within isolation windows, and substantial computational requirements for data processing. Method design choices, such as the number and width of windows and cycle time, influence sensitivity and coverage.

SWATH-MS has been widely adopted in proteomics research and clinical studies. Software tools for SWATH analysis include OpenSWATH, Skyline, and other DIA-focused platforms. The approach supports applications ranging from large-scale biomarker discovery to comparative proteomics, often requiring careful library construction and rigorous data processing.