{"id":"W1968063944","doi":"10.1021/pr9006365","title":"Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry","year":2009,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":562,"is_retracted":false,"has_abstract":true,"ca_institutions":"Memorial University of Newfoundland","funders":"National Cancer Institute; U.S. Public Health Service","keywords":"Repeatability; Reproducibility; Chromatography; Proteomics; Biomarker discovery; Tandem mass spectrometry; Peptide; Proteome; Chemistry; Orbitrap; Mass spectrometry; Label-free quantification; Quantitative proteomics; Liquid chromatography–mass spectrometry; Computational biology; Biology; Biochemistry","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":[0.007882781,0.0001663954,0.0003691626,0.0004449664,0.0002148251,0.00009835963,0.0005662884,0.0001726537,0.0001183842],"category_scores_gemma":[0.00168327,0.0001533586,0.0001196742,0.001102924,0.0002828146,0.0003435512,0.00009170522,0.001496113,0.000003399876],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003434734,"about_ca_system_score_gemma":0.0001754096,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002545529,"about_ca_topic_score_gemma":0.000002243917,"domain_scores_codex":[0.9968356,0.000166761,0.0009842658,0.0008588205,0.0006832164,0.0004713319],"domain_scores_gemma":[0.9971119,0.0001255951,0.0003869313,0.001652099,0.0005187546,0.0002047136],"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":[0.0001590266,0.0003286637,0.009128995,0.00008499926,0.0000118716,0.000008581441,0.00006132838,0.000001487352,0.9889142,0.0003532394,0.0002282112,0.0007194023],"study_design_scores_gemma":[0.0004762443,0.0003374526,0.01105263,0.0001445931,0.000007281508,0.0000787439,0.0001105635,0.00003138973,0.9254947,0.06132856,0.0007597241,0.0001781284],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9889677,0.0007383229,0.005397554,0.002853651,0.00001384033,0.000983505,0.00002146,0.00004366748,0.0009803205],"genre_scores_gemma":[0.953152,0.0005354533,0.0456904,0.00001091058,0.0001195696,0.0001808401,0.000005704469,0.00001841119,0.0002867192],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06341951,"threshold_uncertainty_score":0.649995,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03830414990698112,"score_gpt":0.3766268700147317,"score_spread":0.3383227201077506,"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."}}