{"id":"W4407110518","doi":"10.1002/pmic.202400225","title":"Comparative Analysis of Data‐Driven Rescoring Platforms for Improved Peptide Identification in HeLa Digest Samples","year":2025,"lang":"en","type":"article","venue":"PROTEOMICS","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Canada Research Chairs","keywords":"Computer science; Identification (biology); Proteomics; Computational biology; Data mining; Bioinformatics; Biology; Gene; Biochemistry","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001189824,0.0003855654,0.000390241,0.0006947927,0.0003201459,0.0004576063,0.0003206423,0.0003027375,0.0008531579],"category_scores_gemma":[0.001544158,0.0001692564,0.000372324,0.0003712079,0.0001731539,0.0003719956,0.0003359211,0.0002653406,0.0003251233],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003193936,"about_ca_system_score_gemma":0.0003669352,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001518389,"about_ca_topic_score_gemma":0.002839828,"domain_scores_codex":[0.9996856,0.00005540693,0.00002819947,0.00007549073,0.0001221975,0.00003303455],"domain_scores_gemma":[0.9994723,0.0002218549,0.00004410889,0.00005785262,0.0001780578,0.00002592749],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0006591098,0.00005812778,0.004274852,0.0001448871,0.00006315009,0.0001257065,0.00008119116,0.002284435,0.971949,0.0001084441,0.0004535219,0.01979749],"study_design_scores_gemma":[0.00001558066,0.0003362031,0.02276832,0.00001438372,0.00007758982,0.0002504215,0.00009410044,0.04078593,0.9334733,0.0001231935,0.002022097,0.00003903483],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9794605,0.0005701393,0.01706022,0.00007150402,0.00002159031,0.00005401103,0.001303851,0.000793647,0.0006645591],"genre_scores_gemma":[0.8997272,0.0006054426,0.09215507,0.0001053351,0.00001388438,0.0001483707,0.005528925,0.0002937055,0.001422101],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001518389,"threshold_uncertainty_score":0.006292462,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0638963894857469,"score_gpt":0.3686987505385418,"score_spread":0.3048023610527949,"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."}}