Introduction

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.

Publications

  1. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.
    Cite this
    Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G, 2003-01-01 - Rapid communications in mass spectrometry : RCM
  2. PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification.
    Cite this
    Zhang J, Xin L, Shan B, Chen W, Xie M, Yuen D, Zhang W, Zhang Z, Lajoie GA, Ma B, 2012-04-01 - Molecular & cellular proteomics : MCP

Credits

  1. Bin Ma
    Developer

  2. Kaizhong Zhang
    Developer

  3. Christopher Hendrie
    Developer

  4. Chengzhi Liang
    Developer

  5. Ming Li
    Developer

  6. Amanda Doherty-Kirby
    Developer

  7. Gilles Lajoie
    Investigator

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Summary
AccessionBT005425
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByGilles Lajoie