{"id":"W4414048588","doi":"10.1101/2025.09.02.673809","title":"Reverse Proteolysis Uncovers a Hidden Dimension of the Peptidome","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"T-cell and Retrovirus Studies","field":"Immunology and Microbiology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Proteolysis; Cathepsin; Protease; Proteases; Ubiquitin; Lipid-anchored protein","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0003715931,0.0004932944,0.0007832799,0.0002134109,0.0003370151,0.00002214722,0.0007529194,0.0008131682,0.0000890396],"category_scores_gemma":[0.0002676351,0.0003566398,0.0004185435,0.0004998441,0.0004883506,0.00004880277,0.001671588,0.00100236,0.00011053],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001846708,"about_ca_system_score_gemma":0.0005639105,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004319995,"about_ca_topic_score_gemma":0.00001172892,"domain_scores_codex":[0.9977955,0.0003192679,0.0005517268,0.0007476626,0.0001192086,0.0004665938],"domain_scores_gemma":[0.9974896,0.0001005533,0.0005770554,0.001423359,0.0003752038,0.00003419878],"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":[0.0000857527,0.000134646,0.01128512,0.00039537,0.0009769917,0.000005176436,0.00004751614,0.0000133558,0.9824718,0.000352772,0.004228545,0.000002975666],"study_design_scores_gemma":[0.0009412146,0.00006129771,0.03243895,0.0008820613,0.0006092613,1.841411e-8,0.00002475698,0.000002248871,0.9367972,0.000004452786,0.0277004,0.0005381666],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9876336,0.005639692,0.00003968262,0.0005117725,0.004081757,0.001257041,0.0005439097,0.0001917174,0.0001008323],"genre_scores_gemma":[0.9980578,0.000476076,0.0003476513,0.000190154,0.00007570009,0.0001466248,4.244563e-7,0.00003610225,0.0006694788],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04567459,"threshold_uncertainty_score":0.9998885,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008830335909107373,"score_gpt":0.2014791010671269,"score_spread":0.1926487651580195,"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."}}