{"id":"W1974471014","doi":"10.1002/pmic.200600410","title":"Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry","year":2007,"lang":"en","type":"article","venue":"PROTEOMICS","topic":"Ubiquitin and proteasome pathways","field":"Biochemistry, Genetics and Molecular Biology","cited_by":89,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"","keywords":"Ubiquitin; Mass spectrometry; Digestion (alchemy); Chemistry; Proteomics; Bottom-up proteomics; Chromatography; Computational biology; Protein mass spectrometry; Tandem mass spectrometry; Biochemistry; 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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.002018115,0.000287681,0.0003255281,0.000115921,0.0001424417,0.00006667434,0.000318888,0.0003519348,0.000026359],"category_scores_gemma":[0.0004007905,0.0003019011,0.0001430632,0.0001939061,0.0001057817,0.00002256228,0.00006758273,0.0001942361,0.000001369568],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009249122,"about_ca_system_score_gemma":0.0002116387,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002938913,"about_ca_topic_score_gemma":0.00002447926,"domain_scores_codex":[0.9978551,0.00009062724,0.0006199596,0.0005498871,0.0002832946,0.0006010866],"domain_scores_gemma":[0.9984922,0.00002633126,0.0003978742,0.000438313,0.0004634578,0.0001818345],"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":[0.0007211732,0.0001218489,0.0002126971,0.0002908392,0.00004835445,0.000001561398,0.00005732608,0.000007907397,0.9956489,0.0004061662,0.0000998117,0.002383403],"study_design_scores_gemma":[0.001239831,0.002098458,0.000280163,0.00006360067,0.0000275095,0.00001018868,0.0001794571,0.0002033273,0.9928194,0.002209891,0.000514002,0.0003542319],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.672801,0.0002740317,0.3237575,0.00002867755,0.00007079219,0.002063863,0.0005785555,0.00003622268,0.0003894522],"genre_scores_gemma":[0.9477585,0.00004384998,0.05067083,0.00005438399,0.0002759179,0.0002589803,0.0005672722,0.00007076577,0.0002994979],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2749576,"threshold_uncertainty_score":0.9999433,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02299736922849913,"score_gpt":0.307158173679308,"score_spread":0.2841608044508088,"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."}}