Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 17 (20), 2337-42

PEAKS: Powerful Software for Peptide De Novo Sequencing by Tandem Mass Spectrometry

Affiliations

PEAKS: Powerful Software for Peptide De Novo Sequencing by Tandem Mass Spectrometry

Bin Ma et al. Rapid Commun Mass Spectrom.

Abstract

A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.

Similar articles

See all similar articles

Cited by 241 PubMed Central articles

See all "Cited by" articles

Publication types

MeSH terms

LinkOut - more resources

Feedback