{"id":"W3127235909","doi":"10.1021/acs.jproteome.0c00775","title":"Confident Identification of Citrullination and Carbamylation Assisted by Peptide Retention Time Prediction","year":2021,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":20,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Deamidation; Chemistry; Citrullination; Chromatography; Peptide; Mass spectrometry; Hydrophilic interaction chromatography; Citrulline; Arginine; Asparagine; Hydrogen–deuterium exchange; High-performance liquid chromatography; Biochemistry; Amino acid; Enzyme","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":[0.001561627,0.00007440249,0.0001672837,0.0001674878,0.0001266345,0.00006012804,0.0001203902,0.0001274444,0.0001419599],"category_scores_gemma":[0.0004034657,0.00007553508,0.00006450096,0.0003283056,0.00009080126,0.0002722349,0.00004939848,0.000411717,0.000003473926],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000176105,"about_ca_system_score_gemma":0.0001225597,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009836818,"about_ca_topic_score_gemma":7.386392e-7,"domain_scores_codex":[0.9981889,0.0001050961,0.000717831,0.0001767352,0.0006716989,0.0001397647],"domain_scores_gemma":[0.9971584,0.00009108034,0.0006030817,0.0002075207,0.001867584,0.00007229782],"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":[0.00004236108,0.00008491795,0.0006113779,0.0001228818,0.00002285783,0.000002094988,0.00005904098,0.00001049248,0.9952329,0.0003596941,0.0004922544,0.002959131],"study_design_scores_gemma":[0.000367306,0.00006880218,0.002711917,0.0001543443,0.00002051699,0.00006830284,0.0001213328,0.001739961,0.987012,0.006309029,0.001364815,0.00006172063],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9390777,0.0006968412,0.05792098,0.000816747,0.0000252194,0.0003652128,0.00007777233,0.00002472743,0.0009948036],"genre_scores_gemma":[0.9877372,0.0007209184,0.00848546,0.000002762471,0.0001069475,0.00006799788,0.00009887361,0.00001735975,0.002762456],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04943552,"threshold_uncertainty_score":0.3080231,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03925654251946654,"score_gpt":0.3521815087747927,"score_spread":0.3129249662553261,"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."}}