Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry
peer-reviewed · Analytical Chemistry · 2007
| Date | 2007-02-01 |
| Type | peer-reviewed |
| Venue | Analytical Chemistry |
| Publisher | American Chemical Society (ACS) |
| Contribution | adjacent |
| DOI | 10.1021/ac0617013 |
| Citations (OpenAlex) | 214 |
| Venue 2-year citedness | 6.29 |
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.
Methods and tools
- Lookup Peaks: Hybrid de novo sequencing and database-search method for protein identification by tandem MS.
Cites (3)
- De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning (2006) crossref
- Identification of Protein Modifications Using MS/MS de Novo Sequencing and the OpenSea Alignment Algorithm (2005) crossref
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) crossref
Cited by (6)
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- UniNovo: a universal tool for de novo peptide sequencing (2013) both
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- Constrained De Novo Sequencing of Conotoxins (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009) both