FoxNovo

algorithm · Transformer (NAR)

FoxNovo: algorithm · Transformer (NAR). Non-autoregressive de novo sequencer specialised for HLA-I immunopeptides. Uses dual-token m/z encoding (integer + decimal vocabularies, ~4k tokens instead of ~3M…

Non-autoregressive de novo sequencer specialised for HLA-I immunopeptides. Uses dual-token m/z encoding (integer + decimal vocabularies, ~4k tokens instead of ~3M fine-grained bins) in the spectrum encoder, then dynamic-programming top-K decoding over the NAR probability matrix to enforce exact precursor-mass constraints. Reaches >90% peptide accuracy at ~2,800 spectra/s, over 100x faster than the beam-search baseline, and was used to re-analyse 168M spectra from 4,423 raw files in 18 h on one GPU, recovering 41 of 42 targeted-MS-validated non-canonical peptides.

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

Code

• https://github.com/fennomix/fennomix.novo

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Papers

• Accurate and ultra-fast de novo HLA-I immunopeptide sequencing with FoxNovo (2026, LangTaoSha (LTS) Preprint, preprint)

Authors (5)

Ze-Xuan Chen, Chang-Rong You, Ching Tarn, Xie-Xuan Zhou, Wen-Feng Zeng

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