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. Author manuscript; available in PMC: 2009 Nov 10.
Published in final edited form as: Proteomics. 2009 Apr;9(7):1763–1770. doi: 10.1002/pmic.200800282

Figure 1.

Figure 1

Diagram of two-stage MS2/MS3 database search process. The MS2 and MS3 data are searched in two parallel independent database searches. In the first database search stage, MS2 spectral data are searched against a protein database to give a set of peptide and protein identifications for the MS2 data. In the second stage, MS3 spectral data are searched against the same protein database to give the other set of peptide and protein identifications for the MS3 data. Peptide matches for the MS2 and MS3 data are then merged to give the final list of peptide matches for the data set by use of software tools.