Casanovo Foundation

algorithm · Transformer (AR)

Casanovo Foundation: algorithm · Transformer (AR). Foundation model for tandem-MS proteomics: pre-trained the Casanovo spectrum encoder on 30M labelled spectra from MassIVE-KB, then reused the encoder off-the-shelf for…

Foundation model for tandem-MS proteomics: pre-trained the Casanovo spectrum encoder on 30M labelled spectra from MassIVE-KB, then reused the encoder off-the-shelf for downstream tasks (de novo sequencing, spectrum quality, chimericity, phosphorylation, glycosylation prediction). Successor in spirit to Casanovo v1/v2/v5.

Kind	algorithm
Deep learning	yes
Acquisition	DDA
Family	Transformer (AR)

Code

• https://github.com/Noble-Lab/casanovo-foundation

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Paper describing it

• Foundation model for mass spectrometry proteomics (2025, arXiv, preprint)

Authors (8)

Justin Sanders, Melih Yilmaz, Jacob H. Russell, Wout Bittremieux, William E. Fondrie, Nicholas M. Riley, Sewoong Oh, William Stafford Noble

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