Skip to main content
. 2015 Jul 27;14(9):2301–2307. doi: 10.1074/mcp.O114.047035

Fig. 1.

Fig. 1.

Spectrum-centric analysis and peptide-centric analysis. In spectrum-centric analysis, each MS/MS spectrum from either a DDA or DIA experiment is queried against a protein sequence database. The peptides that yield the best scoring N statistically significant PSMs are assigned to the corresponding MS/MS spectrum. Typically N is one for a DDA spectrum and multiple for a DIA spectrum (showing N = 4 here). In peptide-centric analysis, every peptide of interest is queried against the acquired MS/MS data. The bottom-middle panel shows the extracted MS/MS signal of the query peptide over time in which the signal is extracted from any MS/MS spectrum generated from isolating the query precursor m/z. The extraction window width corresponds to the acquisition method, showing here 2 m/z for DDA and 10 m/z for DIA. The precursor m/z of the query peptide is sampled stochastically and sparsely in DDA but systematically in DIA. The MS/MS signal that provides the best scoring evidence of detection is assigned to the query peptide (indicated by the arrows).