Peptide de novo sequencing is the analytical process that derives a peptide’s amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance 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 target peptide. A clear advantage of de novo sequencing is that it works for both database and novel peptides.

Sequence determination of a protein that cannot be found in a sequence database requires de-novo sequencing. De Novo protein sequencing is the process by which the amino acid sequence is deduced without prior knowledge of the DNA or protein sequence. This differs from sequence confirmation, where the protein/DNA sequence is already known and the sequence data obtained is used to confirm that it is correct. De-novo protein sequencing of an intact protein needs careful experimental design, a combination of different analyses and evaluation of data from mass spectrometry, protein chemistry and bioinformatics.