DIA/SWATH (Data-Independent Acquisition)
DIA (Data-Independent Acquisition) — commercially implemented as SWATH-MS by Sciex — fragments all precursor ions in sequential m/z windows simultaneously, giving comprehensive and reproducible peptide quantification from a pre-built spectral library.
Use in this research (from rahali-2022)
- Phase 1 (DDA): ran DDA acquisition on HSA tryptic digests → built spectral library of 127 HSA peptides
- Phase 2 (DIA/SWATH): ran same samples in SWATH mode → quantified all 127 peptides reproducibly; confirmed PTM sites detected by top-down
- Key result: all CLD-relevant isoforms (cysteinylation, glycation, sulfonylation, truncation) confirmed at peptide level
Advantages
- All peptides in the spectral library are quantified in every injection (no stochastic sampling as in DDA)
- Reproducible between runs → enables longitudinal studies and multi-center comparisons
- Sciex TripleTOF 5600+ is used for both ALBOM top-down AND SWATH validation → same instrument family
Limitations
- Requires a pre-built spectral library (DDA phase must precede DIA phase)
- Cannot resolve multi-PTM co-occurrence at protein level (same limitation as all BU methods)
See also
- Bottom-up proteomics — DIA/SWATH is a targeted-quantitative extension of the BU workflow
- rahali-2022 — primary application in this vault