Data dependent acquisition (DDA) is one of the most widely used strategy in shotgun proteomics. Typically, tryptic protein digests are separated by chromatography and the eluting peptides are directly injected into the mass spectrometer. A full scan (MS1) is acquired from which the n most intense precursor peptides are isolated for peptide fragmentation. For each fragmented precursor, a fragment ion spectra (MS2) is recorded. From the m/z of the peptide fragment ions the identity of the precursor peptide is determined. This cycle is repeated across the length of the gradient used to elute the peptides from the analytical column.

Data independent acquisition (DIA, MS-SWATH) is a young and promising technique. In contrast to DDA all precursor ions are fragmented. To do so, the whole mass range is divided into equally sized bins (isolation window of about 10-25 m/z). All precursors in each bin are fragmented simultaneously and during each cycle all bins are scanned sequentially. While the technique promises to facilitate deeper coverage and reduced sparseness of the data in shorter acquisition time, algorithms for the automatic interpretation of such raw data are still in development. Furthermore, such measurements require the use of retention time calibrants and the availability of spectral library of at least the same depth. Ludwig et al.

Other data acquisition strategies:
PRM, MRM, SRM, MaxQuantLive!, BoxCar