When PMF fails, fragments in the CID spectrum can provide crucial information. The data can be used in two ways:

• Uninterpreted fragment ion masses can be used in correlative database searching to identify proteins whose peptides would likely yield similar CID spectra under the same fragmentation conditions. Probability-based matching is used here.
• Peaks of the mass spectrum can be interpreted, either manually or automatically, to derive partial de novo peptide sequences that can be used as standard database queries.