{"id":"W4391822686","doi":"10.1038/s42004-024-01112-7","title":"A spectroscopic test suggests that fragment ion structure annotations in MS/MS libraries are frequently incorrect","year":2024,"lang":"en","type":"article","venue":"Communications Chemistry","topic":"Mass Spectrometry Techniques and Applications","field":"Chemistry","cited_by":32,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","keywords":"In silico; Fragmentation (computing); Chemistry; Tandem mass spectrometry; Mass spectrometry; Collision-induced dissociation; Ion-mobility spectrometry; Ion; Computational biology; Computer science; Chromatography; Biology","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.003218821,0.0007374265,0.0003998044,0.001592981,0.001050032,0.001852505,0.001112051,0.001844179,0.007095508],"category_scores_gemma":[0.02120011,0.0003047798,0.0005078989,0.001804763,0.001194735,0.002245604,0.0009365679,0.001217356,0.003948748],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000654323,"about_ca_system_score_gemma":0.0004977432,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006551747,"about_ca_topic_score_gemma":0.0005913025,"domain_scores_codex":[0.9962234,0.0005672083,0.0003961854,0.001076737,0.001467228,0.0002691532],"domain_scores_gemma":[0.9784775,0.009273124,0.005341525,0.003854505,0.002640165,0.000413202],"domain_codex":null,"domain_gemma":"methods","domain_candidate":"methods","domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.003947662,0.0005120441,0.07234252,0.0008170722,0.0003948552,0.005995549,0.001051679,0.009360558,0.7974285,0.007797296,0.008396278,0.09195594],"study_design_scores_gemma":[0.0001486351,0.0009892904,0.03966594,0.0001885039,0.0002629371,0.01038173,0.0007848945,0.04051146,0.8575476,0.01095862,0.0384062,0.0001541801],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8862569,0.001159133,0.08986779,0.002981603,0.000557341,0.0001246332,0.00346451,0.007449985,0.008138169],"genre_scores_gemma":[0.9402061,0.000230954,0.05159412,0.001386063,0.00005586528,0.00004992139,0.003888197,0.0008167081,0.001772281],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9967812,"threshold_uncertainty_score":0.02373689,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01706788419027487,"score_gpt":0.2749302783235082,"score_spread":0.2578623941332333,"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."}}