π-SPECFormer
algorithm · Transformer (AR)
π-SPECFormer: algorithm · Transformer (AR). Mass-spectrometry foundation model: a 21M-parameter Transformer spectrum encoder pre-trained contrastively (MoCo-style, InfoNCE over masked-peak views) on 178M…
Mass-spectrometry foundation model: a 21M-parameter Transformer spectrum encoder pre-trained contrastively (MoCo-style, InfoNCE over masked-peak views) on 178M unidentified spectra, then refined on 114M PSMs grouped by precursor. For de novo sequencing the frozen encoder feeds a task-specific Transformer encoder and autoregressive peptide decoder; the same embeddings serve spectrum clustering and, fine-tuned, PTM detection. Applied to mine single-amino-acid variants from dark spectra in a 103-patient lung adenocarcinoma cohort.
| Kind | algorithm |
| Deep learning | yes |
| Acquisition | DDA |
| Family | Transformer (AR) |
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.
Trained on
- IPX0001804000 (as deposited)
Evaluated on
- IPX0001804000 (as deposited)
- Nine-species benchmark (original (DeepNovo, 2017))
Paper describing it
- π-SPECFormer: A Mass Spectrometry-based Foundation Model for Decoding the Dark Proteome (2026, bioRxiv, preprint)