Figure 1.

The workflow of Crystal-C as applied to each PSM from open search results. A) Find potential missed cleavage sites by searching the previous and next fully-enzymatic peptides of the identified peptide, where M^Tol is the mass tolerance (20 ppm by default), M^E is the precursor neutral mass, M^T is the identified peptide mass, and M^P and M^N are the previous and next adjacent fully enzymatic peptide masses, respectively. B) Check whether the PSM is semi-enzymatic by deleting one amino acid from the left or right side of the identified peptide sequence at a time and calculating the mass difference between M^E and the remaining peptide sequence. If the mass difference is smaller than M^Tol, the remaining peptide sequence is regarded as semi-enzymatic. C) Find chimeric MS/MS spectra. Crystal-C searches for peaks from the identified peptide within the isolation window by comparing theoretical isotopic clusters (purple)to the MS1 spectrum. If a peak matching one of the theoretical isotope clusters is found in the isolation window and does not belong to the precursor, the PSM is considered chimeric.