Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry

peer-reviewed · Analytical Chemistry · 2007

peer-reviewed · Analytical Chemistry · 2007. Marshall Bern et al. A powerful technique for peptide and protein identification is tandem mass spectrometry followed by database…
Date 2007-02-01
Type peer-reviewed
Venue Analytical Chemistry
Publisher American Chemical Society (ACS)
Contribution adjacent
DOI 10.1021/ac0617013
Citations (OpenAlex) 207
Venue 2-year citedness 7.10

Abstract

A powerful technique for peptide and protein identification is tandem mass spectrometry followed by database search using a program such as SEQUEST or Mascot. These programs, however, become slow and lose sensitivity when allowing nonspecific cleavages or peptide modifications. De novo sequencing and hybrid methods such as sequence tagging offer speed and robustness for wider searches, yet these approaches require better spectra with more complete and consecutive fragmentation and, hence, are less sensitive to low-abundance peptides. Here we describe a new hybrid method that retains the sensitivity of pure database search. The method uses a small amount of de novo analysis to identify likely b- and y-ion peaks–“lookup peaks”–that can then be used to extract candidate peptides from the database, with the number of candidates tunable to fit a computing budget. We describe a program called ByOnic that implements this method, and we benchmark ByOnic on several data sets, including one of mouse blood plasma spiked with low concentrations of recombinant human proteins. We demonstrate that ByOnic is more sensitive than sequence tagging and, indeed, more sensitive than the three most popular pure database search tools–SEQUEST, Mascot, and X!Tandem–on both the peptide and protein levels. On the mouse plasma samples, ByOnic consistently found spiked proteins missed by the other tools.

Authors

  1. Marshall Bern · Palo Alto Research Center, Protein Metrics (United States), Protein Metrics Inc.
  2. Yuhan Cai · Palo Alto Research Center
  3. David Theo Goldberg · Palo Alto Research Center

Methods and tools

  • Lookup Peaks: Hybrid de novo sequencing and database-search method for protein identification by tandem MS.

Cites (5)

Cited by (18)

Seen in the charts

Back to the full map

Back to top