Quantification of proteins can be performed by means of mass spectrometry either in data-dependent acquisition or data-independent acquisition. For quantification by means of DDA, it is crucial to have 8-10 datapoints over the elutionprofile of a peptide. This can be obtained by adapting the cycle time.
In SWATH, the entire m/z range is divided in different ‘swaths’ or windows. The entire range of m/z values is covered in a few seconds. In each window all precursors are fragmented leading to quantitative information on all precursors. Identification of these precursors is obtained via matching of the spectra with a library built from DDA runs.
Ion mobility-assisted data independent acquisition MS or HDMSE is a second way to perform DIA experiments. In HDMSE, no windows are present but all precursors from the entire m/z range are fragmented at a certain time point. No DDA library is necessary for identification since fragments and precursors can be linked to one another through ion mobility separation. This DIA method is preferred when low amount of sample is available.
Besides label-free, quantification by means of iTRAQ or SILAC can be achieved as well.