De novo sequencing of peptides

De novo sequencing involves deducing a peptide's sequence purely from mass spectral fragmentation data. There are roughly two ways to view the relationship between de novo sequencing and database search algorithms. First is complementary, and the second is alternative. Approaches that emphasize the complementary relationship between de novo sequences and database searches treat de novo sequences as a means to enhance the quality and reliability of database searches. Regimes originating from this approach utilize the spectra to derive one or more highly reliable sequence tags. These tags guide the database matching process, and since they ostensibly represent the most prominent and reliable features of the spectra, the tags also impart a higher degree of confidence to the database results. De novo sequencing approaches also differ according to the way in which they determine the fragment type (y or b) and score the sequence information. These differences in approach tend to generate great differences between de novo sequences obtained even from the same spectra. There are two principal approaches to the implementation of partial de novo sequencing called the global and local paradigms.