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Figure 3
Schematic comparison of mass-spectrometric data-acquisition methodologies. (a) DDA: precursors identified in the first MS1 stage are selected for MS2 fragmentation on the basis of abundance. Software matches the masses to the database (in silico `trypsinized' proteins). This is the standard discovery mode allowing the identification of novel proteins and phosphorylation sites. (b) SRM: precursors chosen on basis of prior discovery experiments in the MS1 stage; following fragmentation, signature MS2 peaks are also selected. The integration of these transitions can be used for quantitation. (c) DIA: no precursor selection in the MS1 stage; instead, all ions in wide overlapping mass windows (typically 25 mass units) over the whole mass range (from 400 to 1200 m/z) are fragmented. Using spectral libraries obtained in DDA experiments, MS2 spectra corresponding to specific peptides can be extracted.

IUCrJ
Volume 4| Part 2| March 2017| Pages 119-130
ISSN: 2052-2525
https://doi.org/10.1107/S2052252516020546