{"id":"W3205913007","doi":"10.3791/63052","title":"Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis","year":2021,"lang":"en","type":"article","venue":"Journal of Visualized Experiments","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Centre Hospitalier Universitaire Sainte-Justine","funders":"Fonds de Recherche du Québec - Santé; Natural Sciences and Engineering Research Council of Canada; Université de Montréal; Canadian Institutes of Health Research; Monash University","keywords":"Major histocompatibility complex; MHC class I; Computational biology; CD74; Mass spectrometry; Workflow; Antigen processing; Sample preparation; Computer science; Biology; Chemistry; Antigen; Chromatography; Immunology; Database","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":[],"consensus_categories":[],"category_scores_codex":[0.0002773961,0.0001183745,0.0003655106,0.000136442,0.0001007231,0.00004044058,0.00007887117,0.00009699479,0.000009620604],"category_scores_gemma":[0.00008258696,0.0001071192,0.0001806936,0.0001449032,0.0000298551,0.00001903905,0.00008177641,0.00005696987,6.557543e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002072304,"about_ca_system_score_gemma":0.00003447781,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000005941631,"about_ca_topic_score_gemma":0.000002070511,"domain_scores_codex":[0.999058,0.00004315974,0.0005462957,0.0001116147,0.0001150739,0.0001258441],"domain_scores_gemma":[0.9990125,0.00001437357,0.0005569236,0.0001314191,0.0002367172,0.00004808474],"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":[0.0001677833,0.0001499051,0.003500243,0.00002167673,0.001452323,4.671926e-7,0.0002797419,0.00001417751,0.9941599,0.00009448784,0.000117857,0.00004138349],"study_design_scores_gemma":[0.00308306,0.0008634303,0.002910366,0.00002244677,0.0003175907,0.00001131905,0.001297265,0.0006074799,0.9904258,0.00008028378,0.0002501753,0.0001308261],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9915996,0.002463464,0.005709764,0.00002046997,0.00003337546,0.00008408365,0.00001480181,0.000001638173,0.00007283787],"genre_scores_gemma":[0.9885455,0.0004936694,0.01051355,0.00003383903,0.00003665927,0.000003264079,0.00008591944,0.00001291205,0.0002747331],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004803788,"threshold_uncertainty_score":0.4368194,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01783345738888023,"score_gpt":0.3528244850907102,"score_spread":0.33499102770183,"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."}}