Analysis and Annotation of c-Type Ions in Peptide Mass Spectral Libraries

The large collection of high-quality mass spectra in the NIST Human HCD Peptide and NIST Tandem Mass Spectral Libraries is used to understand the role of peptide sequence in c-type ion formation in beam-type collision-induced dissociation. Furthermore, results from the analyses were used to inform and apply annotation rules for c-type ions in the updated Human HCD Peptide Mass Spectral Library. As a result, 155,663 c-type ions are now annotated, providing additional peptide sequence information, often where b- and y-type ions may be lacking. Examples shown here highlight the significance of these c-type ions, both in terms of their relative abundance and in resolving peptide-sequence ambiguities. Furthermore, these examples illustrate the value of including c-type ions to improve searching and scoring of peptide spectrum matches.