{"id":"W3196705307","doi":"10.1021/acs.jproteome.1c00490","title":"Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard","year":2021,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":84,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"","keywords":"Computer science; Workflow; Software; Benchmarking; Data mining; Proteomics; Quantitative proteomics; Proteome; Bioinformatics; Database; Chemistry; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.03582653,0.002812926,0.001629652,0.007715189,0.002317026,0.00379243,0.003724075,0.001468606,0.004183744],"category_scores_gemma":[0.04967178,0.001407847,0.002007648,0.005487765,0.001246992,0.003067436,0.005712704,0.002340864,0.004653911],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001798265,"about_ca_system_score_gemma":0.002429892,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001930349,"about_ca_topic_score_gemma":0.001883481,"domain_scores_codex":[0.9821202,0.002807716,0.003623784,0.003189234,0.007259355,0.0009995956],"domain_scores_gemma":[0.9653187,0.009744436,0.0019232,0.009822969,0.012288,0.0009025719],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.006118863,0.001954199,0.04641874,0.004491298,0.001663512,0.0008671526,0.002162392,0.03563385,0.4004061,0.009560938,0.05124243,0.4394804],"study_design_scores_gemma":[0.0003525563,0.001459278,0.05583185,0.0009206393,0.0004123212,0.001283907,0.0007400754,0.1344267,0.6875712,0.007709028,0.1083812,0.000911333],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.2953648,0.004507801,0.582327,0.000960386,0.0009123983,0.002987103,0.02603695,0.07403114,0.01287236],"genre_scores_gemma":[0.2322492,0.002714718,0.6709908,0.0005462239,0.0001067253,0.005398795,0.06409424,0.02078064,0.003118714],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.03582653,"threshold_uncertainty_score":0.1894711,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1608773151448786,"score_gpt":0.4830560024603403,"score_spread":0.3221786873154617,"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."}}