De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation
peer-reviewed · Electrophoresis · 2009
| Date | 2009-11-01 |
| Type | peer-reviewed |
| Venue | Electrophoresis |
| Publisher | Wiley |
| Contribution | algorithm |
| DOI | 10.1002/elps.200900332 |
| Citations (OpenAlex) | 57 |
| Venue 2-year citedness | 1.93 |
Abstract
De novo sequencing of peptides using tandem MS is difficult due to missing fragment ions in the spectra commonly obtained after CID of peptide precursor ions. Complementing CID spectra with spectra obtained in an ion-trap mass spectrometer upon electron transfer dissociation (ETD) significantly increases the sequence coverage with diagnostic ions. In the de novo sequencing algorithm CompNovo presented here, a divide-and-conquer approach was combined with an efficient mass decomposition algorithm to exploit the complementary information contained in CID and ETD spectra. After optimizing the parameters for the algorithm on a well-defined training data set obtained for peptides from nine known proteins, the CompNovo algorithm was applied to the de novo sequencing of peptides derived from a whole protein extract of Sorangium cellulosum bacteria. To 2406 pairs of CID and ETD spectra contained in this data set, 675 fully correct sequences were assigned, which represent a success rate of 28.1%. It is shown that the CompNovo algorithm yields significantly improved sequencing accuracy as compared with published approaches using only CID spectra or combined CID and ETD spectra.
Methods and tools
- CompNovo: De novo sequencing algorithm combining complementary CID and ETD tandem MS spectra.
Cites (14)
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) crossref
- De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007) crossref
- De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning (2006) crossref
- Proteomics-Grade de Novo Sequencing Approach (2005) crossref
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) crossref
- A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry (2003) crossref
- New computational approaches for de novo peptide sequencing from MS/MS experiments (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
- Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (2000) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) crossref
Cited by (15)
- De Novo Peptide Sequencing for Data-independent Acquisition (DIA) Using Deep Learning (2025) crossref
- PepGo: a deep learning and tree search-based model for de novo peptide sequencing (2025) crossref
- Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
- Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation (2017) both
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs (2016) both
- De novo peptide sequencing using CID and HCD spectra pairs (2016) crossref
- Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets (2016) crossref
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem (2012) both
- De Novo Sequencing and Homology Searching (2012) both
- ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010) crossref
- Dimethyl isotope labeling assisted de novo peptide sequencing (2010) crossref
- Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR (2010) semanticscholar