Poster: De novo protein identification by dynamic programming
abstract · 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) · 2011
abstract · 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) · 2011. Jason Gallia et al. In this paper we present a new de novo method to identify protein and peptide amino acid sequences from…
| Date | 2011-02-01 |
| Type | abstract |
| Venue | 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) |
| Publisher | IEEE |
| Contribution | algorithm |
| DOI | 10.1109/iccabs.2011.5729896 |
| Citations (OpenAlex) | 2 |
Abstract
In this paper we present a new de novo method to identify protein and peptide amino acid sequences from tandem mass spectrometry (MS/MS) data. Our approach uses an integer knapsack dynamic programming formulation, which allows for optimization to directly consider ions other than the typical b and y variety. Rather than acting as “noise” which obscures the sequence in question, the additional ions can be used to improve identifications, and provide greater confidence in the results. We validate our approach using raw experimental data.
Methods and tools
- Knapsack DP de novo sequencing: Formulates de novo sequencing as an integer knapsack dynamic program so that ions other than b and y contribute to the score.