{"paper":{"title":"pUniFind: a unified large pre-trained deep learning model pushing the limit of mass spectra interpretation","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"cs.LG","authors_text":"Han Wen, Hao Chi, Jiale Zhao, Jiaxiang Ding, Kaifei Wang, Pengzhi Mao, Ranfei Chen, Shuqi Lu, Weijie Zhang, Weinan E, Xiaohong Ji, Xin Zhang, Yaping Peng, Yiming Li, Yucheng Liao","submitted_at":"2025-06-30T08:32:39Z","abstract_excerpt":"Deep learning has advanced mass spectrometry data interpretation, yet most models remain feature extractors rather than unified scoring frameworks. We present pUniFind, the first large-scale multimodal pre-trained model in proteomics that integrates end-to-end peptide-spectrum scoring with open, zero-shot de novo sequencing. Trained on over 100 million open search-derived spectra, pUniFind aligns spectral and peptide modalities via cross modality prediction and outperforms traditional engines across diverse datasets, particularly achieving a 42.6 percent increase in the number of identified pe"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2507.00087","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2507.00087/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}