A neural network approach to the identification of b-/y-ions in MS/MS spectra
peer-reviewed · 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · 2012
peer-reviewed · 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · 2012. James Paul Cleveland et al.
| Date | 2012-10-01 |
| Type | peer-reviewed |
| Venue | 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) |
| Publisher | IEEE |
| Contribution | adjacent |
| DOI | 10.1109/BIBM.2012.6392625 |
Methods and tools
- b-/y-ion staged neural network: Staged neural network that models ion fragmentation patterns and estimates the posterior probability of each ion type, used to pick the informative peaks out of an MS/MS spectrum before sequencing. The motivation is search-space control: too many peaks and the candidate peptide space grows exponentially, too few and the ion ladder has gaps that can only be explained by permutations of amino acid combinations, so either way candidate quality drops. Reported to beat other preprocessing techniques and to cut the candidate search space substantially without losing candidate quality. The authors note the step matters to any interpretation of MS/MS spectra, de novo or not. Two papers a year apart: the BIBM 2012 classifier, and the two-stage version in Proteome Science 2013 that states it improves on it.