De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation
peer-reviewed · Analytical Chemistry · 2004
| Date | 2004-09-15 |
| Type | peer-reviewed |
| Venue | Analytical Chemistry |
| Publisher | ACS |
| Contribution | algorithm |
| DOI | 10.1021/ac0491206 |
| Citations (OpenAlex) | 75 |
| Venue 2-year citedness | 6.29 |
Abstract
Mass spectrometry-based de novo peptide sequencing is generally more reliable on high-resolution instruments owing to their high resolution and mass accuracy. On a lower resolution instrument such as the more widely used quadrupole ion traps, de novo peptide sequencing is not so reliable or requires more MS(3) experiments. However, the peptide CID spectrum has been demonstrated to be quite reproducible on an ion trap instrument and can be predicted with good accuracy. A new de novo peptide sequencing technique, DACSIM, combining a divide-and-conquer algorithm for deriving sequence candidates and spectrum simulation for sequence refinement, is developed for spectra acquired on an ion trap instrument. When DACSIM was used to sequence peptides 500-1900 u in mass generated from proteolytic digests of hemoglobin and myoglobin, the success rate was 70% with a false positive rate of only 6%, when isoleucine and leucine residues were not distinguished.
Methods and tools
- DC-Novo: Divide-and-conquer + spectrum simulation
Cites (8)
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- Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing (2025) crossref
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- De novo peptide sequencing by deep learning (2017) crossref
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Peptide de novo sequencing of mixture tandem mass spectra (2016) both
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) both
- De Novo Sequencing and Homology Searching (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010) crossref
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) crossref
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
- A mixed-integer optimization framework for de novo peptide identification (2007) crossref
- De novo peptide sequencing using exhaustive enumeration of peptide composition (2006) crossref
- De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning (2006) crossref