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. Author manuscript; available in PMC: 2017 Aug 14.
Published in final edited form as: Anal Chem. 2017 Apr 17;89(12):6367–6376. doi: 10.1021/acs.analchem.7b00212

Figure 5. Using phosphate losses from fragment ions improves phosphosite localization with AI-ETD.

Figure 5

a) phosphoRS software was modified to use phosphate losses from product ions in ETD spectra to aid phosphosite localization. The percent gain in the number of localized phospho PSMs after modifying phosphoRS is shown for AI-ETD conditions. Using phosphate losses from different combinations of production types (c- and z-type ions only, b- and y-type ions only, and all four ion types) provides varying gains, with the biggest increase achieved when considering losses from all four ion types. b) The number of localized phospho PSMs for ETD, ETciD, EThcD, and AI-ETD conditions are compared when not considering any neutral losses in the phosphosite localization calculation or when enabling use of phosphate losses from product ions in ETD spectra.