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. Author manuscript; available in PMC: 2022 Sep 28.
Published in final edited form as: Biochemistry. 2021 Sep 7;60(38):2902–2914. doi: 10.1021/acs.biochem.1c00369

Figure 3. Verifying the accuracy of ionFinder and envoMatch using an established “true” and “false” dataset.

Figure 3.

A) Fragmentation spectra from 100 Cit-containing and 100 non-Cit containing synthetic peptides that contain confirmed deamidation events from Lee et al,14 were analyzed by ionFinder, envoMatch, or both. The number of verified “true” and “false” hits that fell into each category by ionFinder and envoMatch are shown. B) Representative fragmentation spectra from peptides classified as “true”, “likely”, and “ambiguous” by ionFinder. C) 2644 PSMs from a complex proteomic analysis were analyzed by ionFinder, envoMatch, or both. The number of verified “true” and “false” hits that fell into each category by ionFinder and envoMatch are shown.