{"id":"W4411707447","doi":"10.1038/s41587-026-03116-1","title":"Zero-Shot De Novo Peptide Sequencing with Open Post-Translational Modification Discovery","year":2025,"lang":"en","type":"preprint","venue":"Nature Biotechnology","topic":"Chemical Synthesis and Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"Bioinformatics Solutions (Canada); University of Waterloo","funders":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","keywords":"Zero (linguistics); Computational biology; Computer science; Biology; Philosophy","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.0001857063,0.0003123067,0.000363907,0.000147696,0.00009045286,0.0001081187,0.001110589,0.003341193,0.00001537414],"category_scores_gemma":[0.0001811356,0.0002665707,0.0001766922,0.0001950883,0.0001583439,0.000007402219,0.0009395732,0.001299095,0.000002088759],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001086632,"about_ca_system_score_gemma":0.0006358218,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001629129,"about_ca_topic_score_gemma":0.0002613089,"domain_scores_codex":[0.9983164,0.00004602693,0.0002684229,0.0009185726,0.0001544193,0.0002961548],"domain_scores_gemma":[0.9987346,0.00002663831,0.000184647,0.0008522204,0.0001529011,0.00004898651],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001521679,0.00005717055,0.0005510629,0.00007163242,0.0003171424,0.000006430947,0.00001297534,0.0004968447,0.992551,0.003052401,0.0004353313,0.002295901],"study_design_scores_gemma":[0.0003231548,0.00006569699,0.0003907803,0.000154545,0.0001730061,0.00002904831,0.00004149001,0.0001970642,0.9787948,0.002209474,0.01719047,0.0004304711],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9453021,0.003097127,0.03421788,0.01238574,0.0001558119,0.0006473147,0.0007247217,0.00009170538,0.003377563],"genre_scores_gemma":[0.9864864,0.0003838741,0.009131105,0.000745819,0.0001343418,0.0000745234,0.001770188,0.00002375225,0.001250044],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04118422,"threshold_uncertainty_score":0.9999787,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01368220203031667,"score_gpt":0.2864098803748288,"score_spread":0.2727276783445122,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}