InstaNovo glycopeptide fine-tuning
downstream-application · Transformer (AR)
Adaptation of InstaNovo, a transformer de novo peptide sequencer, to glycoproteomics by fine-tuning on glycopeptide spectra. Learning from glyco spectra is measurable but limited, and every fine-tuning setting suffers catastrophic forgetting, losing accuracy on peptides the base model handled well; fine-tuning on unfiltered spectra that partly overlap the original training set gives the strongest learning signal but does not remove the effect. PCA of spectrum embeddings shows a large domain shift that explains the difficulty, and the study argues for treating overlapping glyco spectra as informative examples rather than outliers to discard, alongside multi-task and contrastive objectives and embedding transformations that pull glyco spectra toward the original distribution.
| Kind | downstream-application |
| Deep learning | yes |
| Acquisition | DDA |
| Family | Transformer (AR) |
| Application area | Glycoproteomics |