In a tandem mass spectrometer, the peptide is fragmented along the peptide backbone and the resulting fragment ions are measured to produce the MS/MS spectrum. Depending on the fragmentation method used, different fragment ion types can be produced. de novo Peptide sequencing derives an amino acid sequence from a mass spectrum without the need of a sequence database. It is in contrast to another popular peptide identification approach – “database search”, which searches in a given database to find the largest peptide. De novo peptide sequencing is the only choice when the sequence database is not available. This makes PEAKS the preferred method for identifying novel peptides and proteins from unsequenced organisms.
PEAKS uses a comprehensive scoring system to provide accurate de novo peptide sequencing results. Unique to PEAKS is the Local Confidence Score – the likelihood of each amino acid assignment in a resultant peptide. The local confidence score extends the accuracy to the amino acid level. In the figure, TLCDEFKADEK is a confident sequence tag with significant fragment proof.
Protein sequences could be obtained from the de novo peptide sequences. The confident de novo peptide sequence tags, which have direct fragmentation ion proof, were assembled into protein sequences, See PEAKS AB Software.