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 | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1016/j.jasms.2006.03.007 |
| Citations (OpenAlex) | 32 |
| Venue 2-year citedness | 2.84 |
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 (10)
- Enhancing TOF/TOF-based de Novo Sequencing Capability for High Throughput Protein Identification with Amino Acid-Coded Mass Tagging (2005) crossref
- De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) crossref
- De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by Fourier transform ion cyclotron resonance mass spectrometry (2004) crossref
- De novo sequencing of novel neuropeptides directly from Ascaris suum tissue using matrix‐assisted laser desorption/ionization time‐of‐flight/time‐of‐flight (2003) 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
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Cited by (10)
- DePS: An improved deep learning model for de novo peptide sequencing (2022) semanticscholar
- De novo sequencing of proteins by mass spectrometry (2020) both
- Lys-Sequencer: An algorithm for de novo sequencing of peptides by paired single residue transposed Lys-C and Lys-N digestion coupled with high-resolution mass spectrometry (2020) crossref
- Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics (2019) 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
- Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry (2010) crossref
- TVNovo: De novo peptide sequencing for high resolution LTQ-FT mass spectrometry using virtual database searching (2010) crossref
- On‐target sample preparation of 4‐sulfophenyl isothiocyanate‐derivatized peptides using AnchorChip Targets (2008) crossref
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) crossref