Figure 2. Tandem mass spectrometry (MS/MS) analysis in data-dependent acquisition and data-independent acquisition ⁵⁰.

( A) Data-dependent acquisition (DDA) acquires MS/MS scans with narrow isolation windows centered on peptide precursors detected in an MS scan over a wide range of masses: 400 to 1,600 mass-to-charge ratio (m/z) here. ( B) Data-independent acquisition (DIA) acquires MS/MS scans with wide isolation windows that do not target any particular peptide precursor. Instead, the scans are arranged side-by-side to collectively cover a desired precursor m/z range (500 to 900 m/z here) comprehensively, and several precursors are fragmented together in a single MS2 event (four here: identified peptide M and peptides N, O, and P). ( C) Fragment ion information for the peptide precursor VLENTEIGDSIFDK++ is present in a single MS/MS spectrum in a DDA analysis, ( D) but it can be extracted over time from DIA data and used for quantification owing to the repetitive MS/MS sampling cycle of DIA. Adapted with permission from Egertson et al. ⁴⁶.