Fragment-ion and amino-acid probability models
adjacent · Transformer (encoder-only)
Two local probability-prediction tasks for tandem mass spectra, aimed at telling sequence-informative fragment evidence from noise and from merely unobserved fragments. Fragment-Ion Probability scores whether a peak-supported mass position is a sequence-informative fragment ion; Amino Acid Probability scores whether two mass-consistent positions are adjacent fragments joined by a candidate residue. Encoder-only Transformers outperform CNN baselines on both, and feeding the probabilities to a separate sequencer raises amino-acid recall, amino-acid precision and peptide recall.
| Kind | adjacent |
| Deep learning | yes |
| Acquisition | DDA |
| Family | Transformer (encoder-only) |
Data
What the papers describing this method trained it on and reported its results on, as each paper states it. A version is named only where the paper names one.
Also used, purpose not recorded
- Nine-species benchmark (version not stated)