PEAKS: powerful software for peptide <i>de novo</i> sequencing by tandem mass spectrometry

TLDR

Protein identification from MS/MS data typically relies on database matching, but this approach fails for unknown genomes and has several drawbacks. The authors present PEAKS, a de novo peptide sequencing software that operates without database dependence. PEAKS employs a novel model and algorithm to identify optimal peptide sequences from MS/MS spectra, providing full‑sequence confidence scores and a positional scoring scheme, and its performance was benchmarked against Lutefisk on Q‑TOF data from standard tryptic peptides. © 2003 John Wiley & Sons, Ltd.

Abstract

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. Copyright © 2003 John Wiley &amp; Sons, Ltd.