Figure 1.

Principles of data-dependent acquisition (DDA) and data-independent acquisition (DIA) in untargeted quantitative proteomics. (A) In DDA, precursor ions are stochastically selected on the basis of their signal intensity in Q1 followed by fragmentation of the selected precursor ions in a collision cell. All fragmented ions are separated and detected by a mass analyzer such as an Orbitrap or time-of-flight (TOF) analyzer. (B) In DIA, all MS1 precursor ions within pre-defined mass windows are selected in Q1 followed by fragmentation of all precursor ions from each window in a collision cell. The resultant MS2 spectra are comprised of fragment ions from all of the precursor ions in the selected Q1 window.