Protein Sequencing with an Adaptive Genetic Algorithm from Tandem Mass Spectrometry
preprint · arXiv · 2008
| Date | 2008-04-08 |
| Type | preprint |
| Venue | arXiv |
| Publisher | arXiv |
| Contribution | algorithm |
| DOI | 10.48550/arXiv.0804.1201 |
| Citations (OpenAlex) | 0 |
Abstract
In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from spectral data (MS and MS/MS spectra). For the moment, our approach only uses MS spectra. A Genetic Algorithm (GA) has been designed with a new evaluation function which works directly with a complete MS spectrum as input and not with a mass list like the other methods using this kind of data. Thus the mono isotopic peak extraction step which needs a human intervention is deleted. The goal of this approach is to discover the sequence of unknown proteins and to allow a better understanding of the differences between experimental proteins and proteins from databases.
Methods and tools
- Adaptive GA for tandem-MS peptide sequencing: Adaptive genetic algorithm for protein sequencing from tandem MS. Represents peptides as GA individuals, evolves them against the observed spectrum; the adaptive component tunes mutation / crossover rates on the fly.