{"id":"W4405989970","doi":"10.1021/acsomega.4c05624","title":"Selected Ion Extraction of Peptides with Heavy Isotopes and Hydrogen Loss Reduces the Type II Error in Plasma Proteomics","year":2025,"lang":"en","type":"article","venue":"ACS Omega","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Toronto Metropolitan University","funders":"Natural Sciences and Engineering Research Council of Canada; Ministry of Science and Technology, Taiwan","keywords":"Chemistry; Electrospray ionization; Peptide; Tandem mass spectrometry; Chromatography; Protein mass spectrometry; Mass spectrum; Mass spectrometry; Stable isotope ratio; Bottom-up proteomics; Analytical Chemistry (journal); 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00006048101,0.0000886311,0.0001092777,0.00003904727,0.0001113041,0.0000116825,0.000116576,0.00007421016,0.000003516744],"category_scores_gemma":[0.00003438229,0.00006514518,0.00001094595,0.0003319909,0.00008314528,0.00007824495,0.00005047978,0.0001677903,4.622363e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003399989,"about_ca_system_score_gemma":0.00005560208,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005278232,"about_ca_topic_score_gemma":0.00003943514,"domain_scores_codex":[0.9995048,0.00000772854,0.0001572504,0.0001660088,0.00005822223,0.000105974],"domain_scores_gemma":[0.999587,0.00004210015,0.00009499804,0.0001877629,0.0000732698,0.00001485825],"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":[0.0001672795,0.00006262107,0.002446576,0.0000479377,0.00001664073,6.496612e-7,0.0001445356,0.0001095631,0.9947551,0.0009041131,0.00007086377,0.001274136],"study_design_scores_gemma":[0.000192676,0.00003908021,0.000440083,0.00008550534,0.00001138014,0.000008941513,0.0001090052,0.0002735821,0.9954711,0.001788094,0.001506336,0.00007417164],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975334,0.00009739539,0.000241343,0.0006390743,0.00000497367,0.0003196706,0.000007169467,0.00004903881,0.001107981],"genre_scores_gemma":[0.9908229,0.0001384267,0.008114804,0.00001831323,0.00001585623,0.0001913275,0.00001114152,0.00001016124,0.0006770464],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007873461,"threshold_uncertainty_score":0.2656543,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009895925398040873,"score_gpt":0.2731780906880391,"score_spread":0.2632821652899982,"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."}}