Table 1.

MS/MS data acquisition modes with their advantages and disadvantages.

MS/MS Data Acquisition Mode	Selection of Precursor Ions	Advantage	Pitfall
Selective or targeted MS/MS	Only selected ions specified on an inclusion list will be targeted	Highest quality MS/MS data	A posteriori acquisition, in a separate batch of analyses
Data-Dependent Acquisition (DDA)	Ions are selected for MS/MS acquisition in real-time based on threshold intensity: Top «n» ions are «picked» in each scan Preferred list and exclusion list	High-quality MS/MS data and established link between precursor and product ions	High acquisition rates required. Selection of the most highly abundant ions each time, across multiple scans, resulting in low MS/MS coverage
Data-Independent Acquisition (DIA)	All fragment ions for all precursors are acquired simultaneously: All-ion-fragmentation (Q1 transmits the full mass range, 50–1700 Da of precursor ions in the collision cell: AIF, MSE) or with sequential mass windows (Q1 transmits several increments of 20–50 amu across the mass range in the collision cell: SWATH, SONAR, BASIC DIA—see Figure 2)	Improved coverage for low abundant precursor ions	High acquisition rates required. Difficulty of MS/MS data deconvolution to re-establish the link between the precursor and product ions