MS-GPT: Rethinking MS/MS De Novo Structure Elucidation as Spectrum-Induced Posterior Querying of a Molecule-Language Model
Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry. Most existing approaches to MS/MS identification remain tied to reference libraries or predefined candidate sets, whereas de novo methods aim to generate structures directly from spectra. A common de novo route predicts a molecular fingerprint from the spectrum and then decodes structures from it, enabling decoder pretraining on large molecule-only corpora. However, this paradigm creates a training-inference mismatch: the decoder is trained on oracle fingerprints computed from molecules, but at inference it is queried with a noisy spectrum-induced fingerprint posterior th...
| Authors | Xin Zhao, Yumin Liu, Zhuo Li et al. |
|---|---|
| Primary category | cs.LG |
| Published | 26 July 2026 |
| Last updated at source | 26 July 2026 |
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