De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation
peer-reviewed · Electrophoresis · 2009
peer-reviewed · Electrophoresis · 2009. Andreas Bertsch et al. De novo sequencing of peptides using tandem MS is difficult due to missing fragment ions in the spectra…
| Date | 2009-11-01 |
| Type | peer-reviewed |
| Venue | Electrophoresis |
| Publisher | Wiley |
| Contribution | algorithm |
| DOI | 10.1002/elps.200900332 |
| Citations (OpenAlex) | 56 |
| Venue 2-year citedness | 2.20 |
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 (15)
- 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
- Fast algorithm for peptide sequencing by mass spectroscopy (1990) crossref
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- Dimethyl isotope labeling assisted de novo peptide sequencing (2010) crossref
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