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. Author manuscript; available in PMC: 2015 Sep 1.
Published in final edited form as: Nat Methods. 2015 Jan 19;12(3):258–264. doi: 10.1038/nmeth.3255

Fig. 2. DIA-Umpire signal processing algorithms.

Fig. 2

The feature detection algorithm is applied to DIA MS1 and MS2 spectra to detect all possible MS1 peptide precursor ions and MS2 fragment signals. Each detected precursor feature is grouped with corresponding co-eluting fragment ion features based on Pearson correlation of LC elution peaks and retention times of peak apexes to form precursor-fragments groups. These precursor–fragment groups are used to construct pseudo MS/MS spectra (separated into different quality tiers based on the quality of detected precursor ion signal) for untargeted spectrum-centric database search and identification. The precursor–fragment groups are stored and are again queried during the second, peptide-centric targeted data extraction stage.