Figure 2.

Types of MS data acquisition modes in bottom-up proteomics. data dependent acquisition (DDA) selects the most abundant peptides which are then isolated and fragmented sequentially. Data Independent Acquisition (DIA) isolates and fragments peptides within defined m/z windows. In targeted acquisition mode, the instrument is set up to detect and fragment selected peptides that are defined a priori. In parallel reaction monitoring (PRM), multiple fragments per precursor can be detected at the same time. In SRM or MRM, fragment ions from a given precursor are typically detected sequentially. Created with biorender.com