{"id":"W4288010073","doi":"10.1021/acs.analchem.2c01036","title":"Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics","year":2022,"lang":"en","type":"article","venue":"Analytical Chemistry","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"H2020 Health; H2020 Marie Skłodowska-Curie Actions; Deutschen Konsortium für Translationale Krebsforschung; Universität Innsbruck; Universitair Medisch Centrum Groningen; HORIZON EUROPE Framework Programme; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Tiroler Wissenschaftsförderung; Universitätsklinikum Hamburg-Eppendorf; Rijksuniversiteit Groningen; Deutsches Krebsforschungszentrum; Stichting TSC Fonds; Deutsche Forschungsgemeinschaft; Ministère de l'Économie, de la Science et de l'Innovation - Québec; European Commission; European Respiratory Society","keywords":"Stable isotope labeling by amino acids in cell culture; Phosphoproteomics; Quantitative proteomics; Robustness (evolution); Computational biology; Tandem mass spectrometry; Proteome; Proteomics; Chemistry; Label-free quantification; Isobaric labeling; Computer science; Biology; Mass spectrometry; Protein phosphorylation; Biochemistry; Phosphorylation; Chromatography","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.03517537,0.002097804,0.001618044,0.005171712,0.0008919979,0.002618216,0.00241814,0.002207785,0.001426227],"category_scores_gemma":[0.04312566,0.001219822,0.001746431,0.003128182,0.001351255,0.001968133,0.002660388,0.002278762,0.000889659],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001915554,"about_ca_system_score_gemma":0.001613124,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001574873,"about_ca_topic_score_gemma":0.001854887,"domain_scores_codex":[0.9671596,0.0103413,0.001901108,0.004049925,0.01578875,0.0007592864],"domain_scores_gemma":[0.9703295,0.01499879,0.002767678,0.002297989,0.009204349,0.0004016644],"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":[0.001916926,0.0002805697,0.009016574,0.004092033,0.0009466801,0.0002434015,0.000954774,0.007118122,0.7742589,0.00647531,0.00204736,0.1926493],"study_design_scores_gemma":[0.00009409842,0.002123979,0.02260375,0.0005872835,0.0009755,0.001391228,0.0004878184,0.05587183,0.8816234,0.005470666,0.02837029,0.0004001436],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.109458,0.04481029,0.8329979,0.001289598,0.001025759,0.00122225,0.001761825,0.002159433,0.005275001],"genre_scores_gemma":[0.2320252,0.01769316,0.7403982,0.0005980208,0.0002963631,0.002605812,0.002560232,0.001053432,0.002769585],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.03517537,"threshold_uncertainty_score":0.1860273,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04900547108992886,"score_gpt":0.443290980720672,"score_spread":0.3942855096307431,"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."}}