InstaNovo-FM

algorithm · Transformer (encoder-only)

InstaNovo-FM: algorithm · Transformer (encoder-only). Self-supervised foundation model for bottom-up proteomics: an encoder-only transformer trained to reconstruct masked regions of tandem mass spectra under a physics-aware…

Self-supervised foundation model for bottom-up proteomics: an encoder-only transformer trained to reconstruct masked regions of tandem mass spectra under a physics-aware objective, over a corpus of 1.47 billion MS/MS spectra with 184.6 million high-confidence annotations. The embeddings capture fragmentation method, sequence properties and post-translational modifications without peptide labels, and support de novo sequencing, database-free identification and analytical run classification as downstream tasks.

Kind	algorithm
Family	Transformer (encoder-only)
Deep learning	yes
Acquisition	DDA

Code

• https://github.com/instadeepai/InstaNovo-FM

Live stars, open issues and last-push figures are on the Code activity chart.

Papers

• Learning from tandem mass spectra at scale with a self-supervised foundation model for proteomics (2026, bioRxiv, preprint)

Authors (12)

Mechiel Nieuwoudt, Marco Reverenna, Divanisha Patel, Rachel Catzel, Isaac H.J. Houngue, Jemma Daniel, Kevin Eloff, Alberto Santos, Nicolas Lopez Carranza, Timothy P. Jenkins, Jeroen Van Goey, Konstantinos Kalogeropoulos

Seen in the charts

• The architectures
• Code activity
• Models and the authors behind them

Back to the full map