{"id":"W2122723562","doi":"10.1021/pr300235v","title":"MS-Simulator: Predicting <i>Y</i>-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions","year":2012,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Mass Spectrometry Techniques and Applications","field":"Chemistry","cited_by":30,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo","funders":"","keywords":"Ion; Tandem mass spectrometry; Mass spectrometry; Computation; Peptide; Identification (biology); Chemistry; Tandem; Biological system; Computer science; Algorithm; Chromatography; Materials science; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002586925,0.0001110792,0.0002387324,0.0002182329,0.0002899027,0.00004867413,0.0002944565,0.00005754289,0.0002881645],"category_scores_gemma":[0.0007212058,0.00006654485,0.00011576,0.0003003101,0.0001510176,0.0001605761,0.0000617646,0.0007408672,0.000001157174],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001345371,"about_ca_system_score_gemma":0.0001238196,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003035774,"about_ca_topic_score_gemma":0.000002639715,"domain_scores_codex":[0.9984174,0.00005889199,0.0003714121,0.0001113832,0.0006718852,0.0003690043],"domain_scores_gemma":[0.9971775,0.0008187168,0.0003232402,0.0003103755,0.00125811,0.0001120668],"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":[0.0007812467,0.0003986337,0.03453333,0.0003709682,0.000104628,0.000002288672,0.0005768906,0.0002681542,0.9467731,0.01443967,0.001398395,0.0003526939],"study_design_scores_gemma":[0.0005029536,0.0004669263,0.001238419,0.0005568237,0.00002487405,0.0000264937,0.001146671,0.008116966,0.9851186,0.001208593,0.001491232,0.0001014964],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9810359,0.00008492419,0.009734082,0.00309855,0.00003296926,0.0006537509,0.00002568924,0.00003306891,0.005301094],"genre_scores_gemma":[0.9948435,0.00001659701,0.004249881,0.00002655216,0.0005288562,0.0001228135,0.000002351234,0.00002174102,0.000187736],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03834544,"threshold_uncertainty_score":0.3218741,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.08261714867255104,"score_gpt":0.3664907465183981,"score_spread":0.283873597845847,"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."}}