{"id":"W2135078307","doi":"10.1074/mcp.m111.010587","title":"PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification","year":2011,"lang":"en","type":"article","venue":"Molecular & Cellular Proteomics","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":1114,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University; University of Waterloo; Bioinformatics Solutions (Canada)","funders":"","keywords":"Computational biology; Identification (biology); Biology; Chemistry; Computer science","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":[0.0004352146,0.0002382872,0.0001993311,0.00006711909,0.000241464,0.00007532845,0.0002504587,0.0001767379,0.00002313895],"category_scores_gemma":[0.00007659022,0.000274991,0.00009550723,0.0001281654,0.0001175038,0.0001531909,0.0001608839,0.0003112657,0.000007716238],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002116634,"about_ca_system_score_gemma":0.0001317185,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009021889,"about_ca_topic_score_gemma":0.000005402852,"domain_scores_codex":[0.998473,0.00004044653,0.0003599755,0.0005685271,0.0001509335,0.0004071392],"domain_scores_gemma":[0.9987505,0.00003595826,0.000191368,0.0006643601,0.0002091505,0.0001486706],"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":[0.00005530503,0.00004135301,0.00005755364,0.0001503211,0.00003232075,0.00004337735,0.0003544603,0.00003157397,0.9951345,0.003373007,0.000007230068,0.0007190512],"study_design_scores_gemma":[0.0003658108,0.00002082465,0.00002601187,0.00005599858,0.00005703155,0.00007132922,0.0002506881,0.005552317,0.9897311,0.003415586,0.0001448054,0.000308436],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.4961626,0.00003543657,0.5024247,0.00003638332,0.000006817183,0.0005929589,0.000106591,0.00009102059,0.0005434835],"genre_scores_gemma":[0.6496008,0.00003042311,0.3491869,0.0000604082,0.00003404574,0.0005439689,0.000284698,0.00005955022,0.000199253],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.1534382,"threshold_uncertainty_score":0.9999702,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04365512402571903,"score_gpt":0.2846905781843063,"score_spread":0.2410354541585872,"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."}}