De Novo Protein Sequencing

De Novo protein sequencing is the process by which the amino acid sequence of a peptide or polypeptide is derived 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 the correctness of the sequence.

De Novo protein sequencing and sequence confirmation are performed by MS/MS. This is a technique in which intact peptides are deliberately fragmented within a mass spectrometer in order to gain structural information from the fragment ions created.

Sequence information can also be obtained by N-terminal sequencing. In this technique amino acids are sequentially removed from the N-terminus of a peptide using Edman Chemistry.

De Novo sequencing is used extensively in the characterisation of biopharmaceutical products and particularity in the characterisation of immunoglobulin variable regions. Another important application is in the identification of unknown proteins in proteomic-type analyses.