de novo Peptide Sequencing
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. Peptide de novo 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 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 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.
Individual Spectrum Sequencing (before)
Complementary Spectra Sequencing (after)
Integrated with Database Search
From de novo Peptide Sequencing to Protein Sequencing
Protein sequences could be obtained from the de novo peptide sequences. The confident de novo sequence tags, which have direct fragmentation ion proof, were assembled into protein sequences, See PEAKS AB Software.
- Ma, B. et al. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom. Rapid Communications in Mass Spectrometry. 17(20):2337-42. 2003.
- He, L. et al. ADEPTS: advanced peptide de novo sequencing with a pair of tandem mass spectra. Journal of Bioinformatics and Computational Biology. 8(06):981-994. 1/12/2012.