{"id":"W4400300730","doi":"10.20517/mrr.2024.21","title":"Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry","year":2024,"lang":"en","type":"article","venue":"Microbiome Research Reports","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa; Health Canada","funders":"","keywords":"Metaproteomics; Workflow; Mass spectrometry; Chromatography; Computer science; Chemistry; Proteomics; Database","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":[0.004444156,0.001539837,0.0009165769,0.001576538,0.0007581973,0.001604823,0.0009348966,0.001082094,0.00150403],"category_scores_gemma":[0.004176386,0.000493677,0.00106787,0.001094475,0.0007457937,0.001197844,0.001386101,0.00133874,0.0009962408],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005680242,"about_ca_system_score_gemma":0.001026582,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007478633,"about_ca_topic_score_gemma":0.001389505,"domain_scores_codex":[0.9969857,0.0004858403,0.0002761809,0.0007261502,0.001300751,0.0002254331],"domain_scores_gemma":[0.9979897,0.0004701398,0.0004277696,0.0003024098,0.0006690233,0.0001409731],"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":[0.000872931,0.0002788336,0.0159989,0.0008212425,0.0002384963,0.0001314086,0.0001675356,0.000911418,0.9566554,0.0002638731,0.0004289853,0.02323104],"study_design_scores_gemma":[0.00004215739,0.001180842,0.04181601,0.0001558413,0.0002707549,0.0007170062,0.000245546,0.01052214,0.9377714,0.0006160628,0.006550476,0.0001118452],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8019499,0.005872161,0.1792799,0.000658158,0.0002659275,0.0007502894,0.005782991,0.002211542,0.003229197],"genre_scores_gemma":[0.678673,0.005351664,0.3017706,0.001117518,0.0001445946,0.001366509,0.00829677,0.0009256365,0.002353665],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004444156,"threshold_uncertainty_score":0.02350318,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06594247374920063,"score_gpt":0.3688041789871602,"score_spread":0.3028617052379596,"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."}}