Figure 3.
Evaluation of the performance of PepQuery for validating completely novel protein sequences. (A) Sensitivity and (B) specificity evaluation for novel peptide sequence validation. Mod. filtering means unrestricted modification searching-based filtering. (C) A spectrum matched to a gold-standard negative peptide without unrestricted modification searching-based filtering. Blue and red colors indicate matched peaks, whereas gray indicates unmatched peaks. (D) The same spectrum in C can be matched to a reference peptide with an ammonium salt modification on aspartic acid with very few unmatched peaks and a high score.
