De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning
peer-reviewed · Journal of Computational Biology · 2006
| Date | 2006-03-01 |
| Type | peer-reviewed |
| Venue | Journal of Computational Biology |
| Publisher | SAGE Publications |
| Contribution | algorithm |
| DOI | 10.1089/cmb.2006.13.364 |
| Citations (OpenAlex) | 58 |
| Venue 2-year citedness | 1.45 |
Abstract
We report on a new de novo peptide sequencing algorithm that uses spectral graph partitioning. In this approach, relationships between m/z peaks are represented by attractive and repulsive springs, and the vibrational modes of the spring system are used to infer information about the peaks (such as “likely b-ion” or “likely y-ion”). We demonstrate the effectiveness of this approach by comparison with other de novo sequencers on test sets of ion-trap and QTOF spectra, including spectra of mixtures of peptides. On all datasets, we outperform the other sequencers. Along with spectral graph theory techniques, the new de novo sequencer EigenMS incorporates another improvement of independent interest: robust statistical methods for recalibration of time-of-flight mass measurements. Robust recalibration greatly outperforms simple least-squares recalibration, achieving about three times the accuracy for one QTOF dataset.
Methods and tools
- EigenMS: Spectral graph partitioning de novo sequencer with robust TOF mass recalibration.
Cites (10)
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
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Cited by (11)
- De novo sequencing of proteins by mass spectrometry (2020) both
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- Constrained De Novo Sequencing of Conotoxins (2012) both
- Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) 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
- Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) crossref
- De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007) crossref
- A mixed-integer optimization framework for de novo peptide identification (2007) crossref