{"id":"W4408572181","doi":"10.1002/pmic.202400238","title":"Monitoring Functional Posttranslational Modifications Using a Data‐Driven Proteome Informatic Pipeline","year":2025,"lang":"en","type":"article","venue":"PROTEOMICS","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Jane ja Aatos Erkon Säätiö; Vetenskapsrådet; Academy of Finland; Svenska Läkaresällskapet; Wellcome Trust","keywords":"Proteomics; Proteome; Computational biology; Pipeline (software); Computer science; In silico; Posttranslational modification; Glycoproteomics; Bioinformatics; Biology; Chemistry; Biochemistry; Gene","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":[0.0001474718,0.0001930159,0.0001730016,0.0001190752,0.0003682005,0.00007512099,0.0005441555,0.0001415112,0.00009005526],"category_scores_gemma":[0.0000815559,0.0002109711,0.00005699028,0.0003173938,0.00007274864,0.0004476009,0.0002260276,0.0003466604,0.00001697645],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001727397,"about_ca_system_score_gemma":0.0002558949,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002643974,"about_ca_topic_score_gemma":0.000001786966,"domain_scores_codex":[0.9986719,0.000009052945,0.0005016307,0.000367479,0.0001993195,0.0002505853],"domain_scores_gemma":[0.9986161,0.000052343,0.0001819968,0.0009032246,0.0001815258,0.00006480409],"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":[0.00008441467,0.0002097728,0.004001609,0.0003832208,0.0000843547,8.562423e-7,0.0001297023,0.01880819,0.9564796,0.01280955,0.0002308882,0.006777854],"study_design_scores_gemma":[0.0006790043,0.000005529105,0.0003242287,0.000311627,0.00007256988,0.00001606671,0.00008034876,0.5863284,0.3856434,0.022534,0.003583416,0.0004213469],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.07574039,0.00008309203,0.9184813,0.0005436375,0.00005556234,0.0007979505,0.000265728,0.0002684069,0.003763905],"genre_scores_gemma":[0.3241968,0.0000403811,0.6736876,0.00004951935,0.0001981465,0.0007246893,0.0003910795,0.00002597003,0.0006858071],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.5708362,"threshold_uncertainty_score":0.8603153,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07659382303852626,"score_gpt":0.3371935030312896,"score_spread":0.2605996799927634,"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."}}