Jornal de Proteômica e Bioinformática

Jornal de Proteômica e Bioinformática
Acesso livre

ISSN: 0974-276X


Methods for Development of De Novo Sequencing Algorithms

Susan Williams

De novo peptide sequencing is the method of determining a peptide amino acid sequence from tandem mass spectrometry in mass spectrometry. For researching the biological activity of a protein, knowing the amino acid sequence of peptides from a protein digest is critical. The Edman degradation process was used in the past to accomplish this. The use of a tandem mass spectrometer to solve peptide sequencing problems is now more widespread. In general, two methodologies are used: database search and de novo sequencing. The database search is a simplified form in which the unknown peptide's mass spectra data is submitted and processed to locate a match with a known peptide sequence, with the peptide with the highest matching score being chosen. Because it can only match to existing sequences in the database, this method fails to recognize novel peptides. The assignment of fragment ions from a mass spectrum is known as de novo sequencing. For interpretation, many algorithms are utilized, and most instruments come with de novo sequencing applications.