Questions What are the rules for mapping peptide sequences to protein sequences?

Generally a peptide is mapped to a protein if the peptide's amino acid sequence is a substring of the protein's sequence. But there are two additional rules:

- Some protein sequences contain the wildcard character X. Every amino acid will match this character. As an example the peptide sequence CDEF will match on the protein sequence ACXEFG.

- Peptide sequences can contain the symbol J, which denotes that the amino acid is either I (Isoleucine) or L (Isoleucine). Js will be matched with both Is and Ls, such that the peptide sequence CJEF will match both the protein sequences ACIEFG and ACLEFG.