De novo peptide sequencing using exhaustive enumeration of peptide composition
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2006
| Date | 2006-08-01 |
| Type | peer-reviewed |
| Venue | Journal of the American Society for Mass Spectrometry |
| Publisher | ASMS |
| Contribution | algorithm |
| DOI | 10.1016/j.jasms.2006.03.007 |
| Citations (OpenAlex) | 32 |
| Venue 2-year citedness | 2.58 |
Abstract
We introduce the use of a peptide composition lookup table indexed by residual mass and number of amino acids for de novo sequencing of polypeptides. Polypeptides of 1600 Daltons (Da) or more can be sequenced effectively through exhaustive compositional analysis of MS/MS spectra obtained by unimolecular decomposition (without CID) in a MALDI TOF/TOF despite a fragment mass accuracy of 50 mDa. Peaks are referenced against the lookup table to obtain a complete profile of amino acid combinations, and combinations are assembled into series of increasing length. Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. While the current work involves measurements acquired on MALDI TOF-TOF, such general treatment of the data anticipates extension to other types of mass analyzers.
Methods and tools
- ENPC: Exhaustive composition enumeration
Cites (7)
- De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- De novo sequencing of peptides using MALDI/TOF-TOF (2002) crossref
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) crossref
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) crossref
- De Novo Peptide Sequencing by Two-Dimensional Fragment Correlation Mass Spectrometry (2000) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref
Cited by (5)
- DePS: An improved deep learning model for de novo peptide sequencing (2022) semanticscholar
- De novo sequencing of proteins by mass spectrometry (2020) both
- Peptide de novo sequencing of mixture tandem mass spectra (2016) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) crossref