PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

peer-reviewed · Rapid Communications in Mass Spectrometry · 2003

peer-reviewed · Rapid Communications in Mass Spectrometry · 2003. Bin Ma et al. A number of different approaches have been described to identify proteins from tandem mass spectrometry…
Date 2003-10-15
Type peer-reviewed
Venue Rapid Communications in Mass Spectrometry
Publisher Wiley
Contribution algorithm
DOI 10.1002/rcm.1196
Citations (OpenAlex) 1388
Venue 2-year citedness 1.80

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.

Authors

  1. Bin Ma · Rapid Novor Inc., University of Waterloo, University of Western Ontario, Western University
  2. Kaizhong Zhang · University of Western Ontario, Western University
  3. Christopher Hendrie · Bioinformatics Solutions Inc.
  4. Chengzhi Liang · Bioinformatics Solutions (Canada), Bioinformatics Solutions Inc.
  5. Ming Li · Bioinformatics Solutions Inc., Central China Institute of Artificial Intelligence, Peng Cheng Laboratory, University of Waterloo, University of Western Ontario
  6. Amanda Doherty-Kirby · University of Western Ontario
  7. Gilles Lajoie · University of Western Ontario, Western University

Methods and tools

  • PEAKS: Commercial DP-based de novo

Cites (10)

Cited by (302)

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