{"id":"pdc-cptac-lscc-discovery-study","title":"CPTAC LSCC Discovery Study","short_title":"PDC000233","aliases":["CPTAC LSCC Discovery Study - Acetylome","CPTAC LSCC Discovery Study - Phosphoproteome","CPTAC LSCC Discovery Study - Proteome","CPTAC LSCC Discovery Study - Ubiquitylome"],"summary":null,"one_liner":null,"identifiers":[{"scheme":"pdc_study_id","value":"PDC000233","url":"https://pdc.cancer.gov/pdc/study/PDC000233","is_primary":true,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000232","url":"https://pdc.cancer.gov/pdc/study/PDC000232","is_primary":false,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000234","url":"https://pdc.cancer.gov/pdc/study/PDC000234","is_primary":false,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000237","url":"https://pdc.cancer.gov/pdc/study/PDC000237","is_primary":false,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"repository":{"name":"NCI Proteomic Data Commons","short_name":"PDC","url":"https://pdc.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[],"program_name":"Clinical Proteomic Tumor Analysis Consortium","program_url":"https://pdc.cancer.gov/pdc/browse","nci_program":"Clinical Proteomic Tumor Analysis Consortium","generating_institutions":[],"data_generation_funding_role":"generation","version":null,"release_date":"2021-01-01","last_upstream_update":null,"retrieved_at":"2026-09-18T02:36:15.354973Z","landing_page_url":"https://pdc.cancer.gov/pdc/study/PDC000233","cancer_types":[{"label":"Lung Squamous Cell Carcinoma","ontology":null,"code":null,"url":null}],"primary_sites":["Bronchus and lung"],"subject":{"scope":"single","tissues":["LUNG"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Lung Squamous Cell Carcinoma; primary_sites: Bronchus and lung","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Repository disease labels or primary sites mapped to pinned tissues."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":115,"n_samples":null,"n_aliquots":800,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"male":88,"female":22,"not reported":5},"race":{"asian":24,"white":71,"other":13,"not reported":6,"black or african american":1},"ethnicity":{"not reported":81,"not hispanic or latino":33,"hispanic or latino":1},"age_at_diagnosis_years":{"n":107.0,"min":40.9,"median":67.0,"max":88.5},"vital_status":{"Dead":34,"Alive":71,"Not Reported":5},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy demographic fields","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"acetylproteome","label":"Acetylome mass spectrometry (TMT11 / DDA)","platform":"TMT11","n_cases":115,"n_samples":217,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"phosphoproteome","label":"Phosphoproteome mass spectrometry (TMT11 / DDA)","platform":"TMT11","n_cases":115,"n_samples":217,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"proteome","label":"Proteome mass spectrometry (TMT11 / DDA)","platform":"TMT11","n_cases":115,"n_samples":217,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"ubiquitylome","label":"Ubiquitylome mass spectrometry (TMT11 / DDA)","platform":"TMT11","n_cases":89,"n_samples":149,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[{"name":"pdc:vital_status","harmonized_name":"demographic.vital_status","label":"Vital status","category":"outcome","n_nonmissing":110,"n_not_reported":5,"n_informative":105,"n_total":115,"coverage_pct":91.3,"populated_pct":95.7,"is_repeated":false,"example_values":["Alive","Dead","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field vital_status over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:cause_of_death","harmonized_name":"demographic.cause_of_death","label":"Cause of death","category":"outcome","n_nonmissing":34,"n_not_reported":12,"n_informative":22,"n_total":115,"coverage_pct":19.1,"populated_pct":29.6,"is_repeated":false,"example_values":["Cancer Related","Unknown","Not Cancer Related","Not Reported","Infection"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field cause_of_death over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:race","harmonized_name":"demographic.race","label":"Race","category":"demographic","n_nonmissing":115,"n_not_reported":6,"n_informative":109,"n_total":115,"coverage_pct":94.8,"populated_pct":100.0,"is_repeated":false,"example_values":["white","asian","other","not reported","black or african american"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field race over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ethnicity","harmonized_name":"demographic.ethnicity","label":"Ethnicity","category":"demographic","n_nonmissing":115,"n_not_reported":81,"n_informative":34,"n_total":115,"coverage_pct":29.6,"populated_pct":100.0,"is_repeated":false,"example_values":["not reported","not hispanic or latino","hispanic or latino"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field ethnicity over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:gender","harmonized_name":"demographic.sex_at_birth","label":"Sex at birth (gender)","category":"demographic","n_nonmissing":115,"n_not_reported":5,"n_informative":110,"n_total":115,"coverage_pct":95.7,"populated_pct":100.0,"is_repeated":false,"example_values":["male","female","not reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field gender over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:morphology","harmonized_name":"diagnoses.morphology","label":"Morphology (ICD-O)","category":"pathology","n_nonmissing":115,"n_not_reported":5,"n_informative":110,"n_total":115,"coverage_pct":95.7,"populated_pct":100.0,"is_repeated":false,"example_values":["8070/3","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field morphology over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:primary_diagnosis","harmonized_name":"diagnoses.primary_diagnosis","label":"Primary diagnosis","category":"diagnosis","n_nonmissing":115,"n_not_reported":5,"n_informative":110,"n_total":115,"coverage_pct":95.7,"populated_pct":100.0,"is_repeated":false,"example_values":["Squamous cell carcinoma, NOS","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field primary_diagnosis over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tissue_or_organ_of_origin","harmonized_name":"diagnoses.tissue_or_organ_of_origin","label":"Tissue or organ of origin","category":"diagnosis","n_nonmissing":115,"n_not_reported":5,"n_informative":110,"n_total":115,"coverage_pct":95.7,"populated_pct":100.0,"is_repeated":false,"example_values":["Lung, NOS","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field tissue_or_organ_of_origin over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tumor_grade","harmonized_name":"diagnoses.tumor_grade","label":"Tumor grade","category":"pathology","n_nonmissing":115,"n_not_reported":5,"n_informative":110,"n_total":115,"coverage_pct":95.7,"populated_pct":100.0,"is_repeated":false,"example_values":["G2","G3","Not Reported","GX","G1"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field tumor_grade over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ajcc_pathologic_stage","harmonized_name":"diagnoses.ajcc_pathologic_stage","label":"AJCC pathologic stage","category":"staging","n_nonmissing":110,"n_not_reported":3,"n_informative":107,"n_total":115,"coverage_pct":93.0,"populated_pct":95.7,"is_repeated":false,"example_values":["Stage IB","Stage IIB","Stage IIA","Stage IIIA","Stage IA","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field ajcc_pathologic_stage over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ajcc_clinical_stage","harmonized_name":"diagnoses.ajcc_clinical_stage","label":"AJCC clinical stage","category":"staging","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":115,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field ajcc_clinical_stage over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tumor_stage","harmonized_name":"diagnoses.ajcc_pathologic_stage","label":"AJCC pathologic stage (tumor_stage)","category":"staging","n_nonmissing":115,"n_not_reported":115,"n_informative":0,"n_total":115,"coverage_pct":0.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field tumor_stage over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:progression_or_recurrence","harmonized_name":"diagnoses.progression_or_recurrence","label":"Progression or recurrence","category":"outcome","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":115,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field progression_or_recurrence over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:last_known_disease_status","harmonized_name":"diagnoses.last_known_disease_status","label":"Last known disease status","category":"outcome","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":115,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field last_known_disease_status over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:prior_treatment","harmonized_name":"diagnoses.prior_treatment","label":"Prior treatment","category":"treatment","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":115,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field prior_treatment over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:prior_malignancy","harmonized_name":"diagnoses.prior_malignancy","label":"Prior malignancy","category":"diagnosis","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":115,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field prior_malignancy over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:synchronous_malignancy","harmonized_name":"diagnoses.synchronous_malignancy","label":"Synchronous malignancy","category":"diagnosis","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":115,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field synchronous_malignancy over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:classification_of_tumor","harmonized_name":"diagnoses.classification_of_tumor","label":"Classification of tumor","category":"pathology","n_nonmissing":110,"n_not_reported":110,"n_informative":0,"n_total":115,"coverage_pct":0.0,"populated_pct":95.7,"is_repeated":false,"example_values":["not reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field classification_of_tumor over 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:age_at_diagnosis","harmonized_name":"diagnoses.age_at_diagnosis","label":"Age at diagnosis","category":"demographic","n_nonmissing":107,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":93.0,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field age_at_diagnosis; a value for 107 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_death","harmonized_name":"demographic.days_to_death","label":"Days to death","category":"outcome","n_nonmissing":34,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":29.6,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field days_to_death; a value for 34 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_last_follow_up","harmonized_name":"diagnoses.days_to_last_follow_up","label":"Days to last follow-up","category":"followup","n_nonmissing":105,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":91.3,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field days_to_last_follow_up; a value for 105 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_recurrence","harmonized_name":"diagnoses.days_to_recurrence","label":"Days to recurrence","category":"outcome","n_nonmissing":4,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":3.5,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: clinicalPerStudy, field days_to_recurrence; a value for 4 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_type","harmonized_name":"diagnoses.treatments.treatment_type","label":"Treatment type","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:24.907161Z","snippet":null,"locator":"PDC000233: paginatedCaseTreatmentsPerStudy, field treatment_type; informative for 0 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.therapeutic_agents","harmonized_name":"diagnoses.treatments.therapeutic_agents","label":"Therapeutic agents","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:24.907161Z","snippet":null,"locator":"PDC000233: paginatedCaseTreatmentsPerStudy, field therapeutic_agents; informative for 0 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_outcome","harmonized_name":"diagnoses.treatments.treatment_outcome","label":"Treatment outcome","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:24.907161Z","snippet":null,"locator":"PDC000233: paginatedCaseTreatmentsPerStudy, field treatment_outcome; informative for 0 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.regimen_or_line_of_therapy","harmonized_name":"diagnoses.treatments.regimen_or_line_of_therapy","label":"Regimen or line of therapy","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:24.907161Z","snippet":null,"locator":"PDC000233: paginatedCaseTreatmentsPerStudy, field regimen_or_line_of_therapy; informative for 0 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_or_therapy","harmonized_name":"diagnoses.treatments.treatment_or_therapy","label":"Treatment given","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":115,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:24.907161Z","snippet":null,"locator":"PDC000233: paginatedCaseTreatmentsPerStudy, field treatment_or_therapy; informative for 0 of 115 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":true,"has_survival_endpoint":true,"survival_endpoints":["overall survival"],"median_followup_months":39.6,"max_followup_months":62.7,"n_cases_with_followup":104,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":false,"response_criteria":[],"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:59.163014Z","snippet":null,"locator":"PDC000233: computed from 115 cases: 34 deaths, 104 with a follow-up time, progression informative for 0","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"access":{"tier":"open","open_components":["4 analytical fraction studies"],"controlled_components":[],"mechanism":"Direct download from the PDC portal or its API; no account required","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the PDC study identifier and the study's primary publication; PDC asks that the consortium be acknowledged.","license":"Open access under the PDC data use terms","publication_policy_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[],"limitations":[],"inappropriate_uses":[],"primary_publications":[],"reuse":[{"publication":{"pmid":"34358469","pmcid":"PMC8475722","doi":"10.1016/j.cell.2021.07.016","title":"A proteogenomic portrait of lung squamous cell carcinoma.","journal":"Cell","year":2021,"authors_short":"Satpathy et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/34358469/","is_open_access":false,"citation_count":367,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["anand s","avanessian s","babur ö","bergstrom e","cao s","carr s","chinnaiyan a","christianson k","cieslik m","clauser k","clinical p","cornwell m","dhanasekaran s","ding l","dou y","fenyö d","geffen y","getz g","gillette m","govindan r","gümüş z","heiman d","hostetter g","huang c","jaehnig e","jean b","jewell s","kane m","krek a","krug k","kumar-sinha c","lei j","liu w","mani d","mani s","mesri m","nesvizhskii a","newton c","omelchenko t","omenn g","paik p","parra e","petralia f","raso m","reva b","robles a","rodrigues f","rodriguez h","ruggles k","satpathy s","savage s","schraink t","schurer s","selvan m","song x","soundararajan r","stathias v","suh j","thiagarajan m","udeshi n","vasaikar s","vats p","visal t","wang p","wen b","wyczalkowski m","zhang b","zhang y","zhu h"],"nci_funded_reuse":true,"linked_grants":["U24CA271037","U24CA210993","U24CA210986","U24CA210985","U24CA210979","U24CA210972","U24CA210967","U24CA210955","U24CA210954","U01CA214125","U01CA214116","U01CA214114","T32CA203690","P30CA240139","P30CA008748"],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000233\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"35264796","pmcid":"PMC8942854","doi":"10.1038/s41586-022-04499-2","title":"Tryptophan depletion results in tryptophan-to-phenylalanine substitutants.","journal":"Nature","year":2022,"authors_short":"Pataskar et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/35264796/","is_open_access":true,"citation_count":121,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["agami r","altelaar m","bassani-sternberg m","bleijerveld o","blommaert n","champagne j","georgiou g","joosten r","kenski j","laos m","lovecchio d","michaux j","mordente k","nagel r","navarro j","nielsen m","olweus j","pak h","pataskar a","peeper d","perrakis a","stone e","van t"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000233\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"38759626","pmcid":"PMC11129317","doi":"10.1016/j.molcel.2024.04.012","title":"Arginine deprivation enriches lung cancer proteomes with cysteine by inducing arginine-to-cysteine substitutants.","journal":"Molecular cell","year":2024,"authors_short":"Yang et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38759626/","is_open_access":true,"citation_count":28,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["agami r","berkers c","bleijerveld o","feng x","jacobs j","montenegro n","paniagua i","pataskar a","yang c","zaal e"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000233\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"39865075","pmcid":"PMC11770092","doi":"10.1038/s41392-025-02128-8","title":"The cryptic lncRNA-encoded microprotein TPM3P9 drives oncogenic RNA splicing and tumorigenesis.","journal":"Signal transduction and targeted therapy","year":2025,"authors_short":"Meng et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/39865075/","is_open_access":true,"citation_count":17,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["cao y","liu d","meng k","pan y","shen h","shi f","shi x","wen n","yuan x","zhang c","zheng d"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000233\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"37517589","pmcid":"PMC10494184","doi":"10.1016/j.mcpro.2023.100626","title":"Pan-Cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics.","journal":"Molecular & cellular proteomics : MCP","year":2023,"authors_short":"Wang et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/37517589/","is_open_access":true,"citation_count":15,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["bullen j","d'angelo g","d'anna r","hurt e","lai z","przybyla a","sidders b","sung m","wang j","wilson m","zhong w"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000233\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"36531007","pmcid":"PMC9753687","doi":"10.3389/fonc.2022.1035188","title":"Inflammation-related citrullination of matrisome proteins in human cancer.","journal":"Frontiers in oncology","year":2022,"authors_short":"Rappu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/36531007/","is_open_access":true,"citation_count":12,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["heino j","rappu p","siljamäki e","suwal u"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000233\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"40488620","pmcid":"PMC12409279","doi":"10.1158/2159-8290.cd-24-1488","title":"Federated Deep Learning Enables Cancer Subtyping by Proteomics.","journal":"Cancer discovery","year":2025,"authors_short":"Cai et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/40488620/","is_open_access":true,"citation_count":11,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"DATA_AVAILABILITY, METHODS","author_keys":["aguilar-mahecha a","aref a","armengol c","balleine r","barranco m","basik m","bowman e","boys e","cai z","clifton-bligh r","connolly e","cooper w","dalal b","dausmann m","defazio a","filipits m","flynn p","george j","gill a","gnant m","graham j","habib r","hains p","harris c","harvey k","horvath l","jackson c","koh j","kohonen-corish m","lim e","liu j","long g","lord r","lucas n","mackenzie k","mann g","mccaughan g","morgan l","murphy l","nagabushan s","nagrial a","navinés j","noor z","panizza b","poulos r","reddel r","robinson p","samra j","scolyer r","souglakos j","swarbrick a","thomas d","williams s","xavier d","zhong q"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000233\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"39633487","pmcid":"PMC11616309","doi":"10.1186/s13073-024-01415-3","title":"SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer.","journal":"Genome medicine","year":2024,"authors_short":"Mora et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/39633487/","is_open_access":true,"citation_count":7,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"DATA_AVAILABILITY, METHODS","author_keys":["balderson b","bodén m","frezza c","mora a","schmidt c"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000233\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"40615674","pmcid":"PMC12283369","doi":"10.1038/s41588-025-02221-2","title":"Cytidine diphosphate diacylglycerol synthase 2 is a synthetic lethal target in mesenchymal-like cancers.","journal":"Nature genetics","year":2025,"authors_short":"Arnoldus et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/40615674/","is_open_access":true,"citation_count":6,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["altelaar m","arnoldus t","bleijerveld o","blomberg n","cabukusta b","dong j","frezza c","giera m","grootemaat a","harkes r","peeper d","piao q","proost n","schatton d","van d","van h","van v"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000233\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"42343131","pmcid":"PMC13384240","doi":"10.1038/s41586-026-10678-2","title":"Alternate RNA decoding results in stable and abundant proteins in mammals.","journal":"Nature","year":2026,"authors_short":"Tsour et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/42343131/","is_open_access":false,"citation_count":5,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"DATA_AVAILABILITY, METHODS","author_keys":["guez j","karczewski k","koo e","leduc a","machné r","slavov n","tsour s","widmer s"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000233\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:27:07.586883Z","snippet":null,"locator":"accession \"PDC000233\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]}],"reuse_metrics":{"n_candidates_screened":19,"n_by_tier":{"t3_analyzed":19,"t2_declared":7,"t1_accession":0,"t0_mention":1},"n_by_tier_raw":{"t3_analyzed":19,"t2_declared":7,"t1_accession":0,"t0_mention":1},"accession_precision":{"token":"PDC000234","query":"METHODS:\"PDC000234\"","strategy_id":"epmc-literal-precision-v1","needs_correction":false,"precision":1.0,"precision_low":1.0,"precision_high":1.0,"n_sampled":0,"n_checked":0,"n_literal":0,"note":"This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":true,"n_verified_reuse":19,"n_reuse_examined":26,"n_independent_reuse":0,"n_nci_funded_reuse":1,"first_reuse_year":2021,"latest_reuse_year":2026,"years_since_release":5.72,"expected_reuse":36.26,"reuse_gap_index":-0.898,"reuse_gap_percentile":28.0,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.735842Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC section-scoped hit counts","retrieved_at":"2026-09-20T18:07:48.735842Z","snippet":null,"locator":"tokens: PDC000233, PDC000232, PDC000234; queries: METHODS:\"PDC000234\"; DATA_AVAILABILITY:\"PDC000234\"; ACCESSION_ID:\"PDC000233\"; REF:\"PDC000234\"","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Index strategy epmc-index-v3. Every dataset is measured with the same single section field per tier, so the counts are comparable; the per-tier value is the largest across the dataset's own accessions, excluding any accession shared with other datasets in the corpus. This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC first-reference dating","retrieved_at":"2026-09-20T18:14:45.119252Z","snippet":null,"locator":"first referenced in 2021 (METHODS section)","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Availability dated from the literature (epmc-first-reference-v2) rather than from repository file timestamps, which record re-harmonization. This is a lower bound on availability."}]},"underexplored":{"is_underexplored":false,"basis":["Reuse is within the expected range for comparable datasets (index -0.90)."],"index_value":-0.898,"percentile":28.0,"comparator_set":"132 datasets in this corpus with a citable accession and sufficient metadata","evidence":[{"method":"derived","source_url":null,"source_label":"Reuse Gap Index (rgi-huber-v2)","retrieved_at":"2026-09-21T02:11:22.976067Z","snippet":null,"locator":"Huber robust regression of log2(analyzing articles + 1) on cohort size, years available, modality breadth and access tier","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Model, covariates and coefficients are published with the dataset export so the label can be recomputed or contested."}]},"grants":[{"core_project_num":"U24CA271037","project_num":null,"title":"Michigan Center for Translational Cancer Proteogenomics","pi_names":["Saravana Mohan Dhanasekaran","Alexey I Nesvizhskii"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":4411659,"org_name":"UNIVERSITY OF MICHIGAN AT ANN ARBOR","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271037","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA271037","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210993","project_num":null,"title":"Systems Biology based Proteogenomic Translator for Cancer Marker Discovery towards Precision Medicine","pi_names":["ERIC E SCHADT","Pei Wang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":4643922,"org_name":"ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210993","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA210993","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210986","project_num":null,"title":"Center of Excellence for High Throughput Proteogenomic Characterization","pi_names":["STEVEN A CARR","MICHAEL A GILLETTE"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":6399756,"org_name":"BROAD INSTITUTE, INC.","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210986","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA210986","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210985","project_num":null,"title":"The Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic Targets","pi_names":["DANIEL Wanyui CHAN","ZHEN ZHANG","Hui Zhang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":5267994,"org_name":"JOHNS HOPKINS UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210985","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA210985","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210979","project_num":null,"title":"Integrated high throughput proteogenomic data analysis center for CPTAC","pi_names":["Chet Birger","GAD A GETZ","Denkanikota R Mani","Michael Noble"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":4417536,"org_name":"BROAD INSTITUTE, INC.","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210979","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA210979","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210972","project_num":null,"title":"Proteogenomic Data Analysis for Cancer Systems Biology and Clinical Translation","pi_names":["Li Ding","David Fenyo","Samuel H Payne"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":3309088,"org_name":"NEW YORK UNIVERSITY SCHOOL OF MEDICINE","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210972","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA210972","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210967","project_num":null,"title":"University of Michigan Proteogenomics Data Analysis Center","pi_names":["ARUL M CHINNAIYAN","Saravana M Dhanasekaran","Alexey I Nesvizhskii"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":4075837,"org_name":"UNIVERSITY OF MICHIGAN AT ANN ARBOR","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210967","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA210967","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210955","project_num":null,"title":"PNNL Proteome Characterization Center","pi_names":["Tao Liu","RICHARD D SMITH"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":5262987,"org_name":"BATTELLE PACIFIC NORTHWEST LABORATORIES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210955","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA210955","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210954","project_num":null,"title":"iPGDAC, An Integrative Proteogenomic Data Analysis Center for CPTAC","pi_names":["Bing Zhang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":4857300,"org_name":"BAYLOR COLLEGE OF MEDICINE","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210954","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U24CA210954","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U01CA214125","project_num":null,"title":"MICROSCALED PROTEOGENOMICS FOR CANCER CLINICAL TRIALS","pi_names":["Meenakshi Anurag","STEVEN A CARR","MATTHEW J ELLIS"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2017,2018,2019,2020,2021],"award_amount_usd":7017736,"org_name":"BAYLOR COLLEGE OF MEDICINE","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA214125","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U01CA214125","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U01CA214116","project_num":null,"title":"Proteogenomic Translational Research Center for Clinical Proteomic","pi_names":["BRIAN J DRUKER","Karin D Rodland"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2017,2018,2019,2020,2021],"award_amount_usd":6816883,"org_name":"BATTELLE PACIFIC NORTHWEST LABORATORIES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA214116","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U01CA214116","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U01CA214114","project_num":null,"title":"Proteogenomic studies aimed at understanding ovarian tumor responses to agents targeting the DNA damage response and translating this knowledge into clinical benefit","pi_names":["Michael Birrer","AMANDA G PAULOVICH"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2017,2018,2019,2020,2021],"award_amount_usd":8409202,"org_name":"FRED HUTCHINSON CANCER CENTER","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA214114","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under U01CA214114","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"T32CA203690","project_num":null,"title":"Translational Breast Cancer Research Training Program","pi_names":["Suzanne AW Fuqua","Mothaffar Fahed Rimawi","MATTHEW J ELLIS"],"agency_ic":"NCI","activity_code":"T32","fiscal_years":[2018,2019,2020,2021,2022],"award_amount_usd":1010160,"org_name":"BAYLOR COLLEGE OF MEDICINE","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=T32CA203690","role":"reuse","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under T32CA203690","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"P30CA240139","project_num":null,"title":"Cancer Research Training and Education Coordination","pi_names":["Kerry L Burnstein","David Benner Lombard","JONATHAN C TRENT","Olveen Carrasquillo","Yan Guo","SION LLEWELYN WILLIAMS","Lauren Ashley Whitmore","Stephen D. Nimer","Eric Wieder","Daniel Bilbao","NIPUN B. MERCHANT","Carl Ola Landgren","Tracy E Crane","ERIN N KOBETZ","Priyamvada Rai","George S. Grills","Frank J Penedo","Dorothy Graves","SOPHIA HL GEORGE","WAEL EL-RIFAI","Barbara A Vance","RAMIN SHIEKHATTAR","Xi Steven Chen","Huw S. Kruger Gray"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":40700595,"org_name":"UNIVERSITY OF MIAMI SCHOOL OF MEDICINE","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA240139","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under P30CA240139","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"P30CA008748","project_num":null,"title":"Cancer Center Administration","pi_names":["ALEX MACDONALD","SELWYN M VICKERS","FRANCESCA M GANY","Hongbiao Carl Lekaye","Elisa de Stanchina","Neeman Mohibullah","Serge K Lyashchenko","Scott Freeswick","Michael Jason de la Cruz","PAUL J SABBATINI","Frances Weis-Garcia","Joachim Silber","MITHAT GONEN","Rui Gardner","YASUHIDE FURUTA","Thomas Michael Atkinson","Nicholas D Socci","Justin Cross","NEIL SCOTT LIPMAN","Ralph J. Garippa","Ouathek Ouerfelli","Charles M. Rudin","Xiuyan Wang","Murray Tipping","Mara Monetti","Gouri Nanjangud","Yehuda Goldgur","Michael H. A. Roehrl","Isabelle Riviere","Ronald Charles Hendrickson","Jason S. Lewis","katia Ognianova manova","Raymond J Muller","Agnes Viale","CRAIG B THOMPSON","PETRUS J HENDRIKX","Carl LeKaye","Isabelle Rivieri","WILLIE H MARK","Marija Drobnjak","HAKIM DJABALLAH","MARGARET A LEVERSHA","RONALD HENDRICKSON","NICHOLAS SOCCI","ANDREW VICKERS","AGNES VIALE","RUI GARDNER","NANJANGUD GOURI","Colin B Begg","Andrew J Vickers","ARIELA NOY","JEANNE RUPERTO","QUATHEK QUERFELLI","Jamie S. Ostroff","MARK G KLANG","JASON Arthur KOUTCHER","MICHEL WJ SADELAIN","NIKOLA P PAVLETICH","VICTOR E REUTER","Victor Reuter","HAROLD E. VARMUS","PAUL TEMPST","ALEX E LASH","WILLIAM L GERALD","LISA K. DENZIN","NEIL LIPMAN","IRENE TSALAPATANIS","ZVI Y. FUKS","ELIZABETH H LACY","CHARLES D LUCARELLI","Felix Homberger","DAVID W GOLDE","Lee A. Niswander","Howard T. Petrie","JOAN MASSAGUE","JANKO Z. NIKOLICH","JAMES ROTHMAN","SCOTT E PERKINS","ELINOR MILLER","JOSEPH Rocco BERTINO","KENNETH J MARIANS","PAUL A MARKS","SIDNEY J WINAWER","ALAN N. HOUGHTON","PAUL LANGNER","RONALD D FINN","Raymond P Warrell","KYOICHI A WATANABE","Raju S.K. Chaganti","RAYMOND NEGRYCZ","STEVEN S STERNBERG","ELIZABETH LACY","PAUL J TEMPST","COLIN B BEGG","DAVID D MYERS"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[1985,1986,1987,1988,1989,1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":717936496,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA008748","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:37:36.955749Z","snippet":null,"locator":"PMID 34358469 reported under P30CA008748","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]}],"access_steps":[{"order":1,"action":"Open the study in the PDC portal","detail":"Proteomic data are released open; the portal's use guidelines still apply. This record spans 4 PDC studies; repeat for each.","url":"https://pdc.cancer.gov/pdc/study/PDC000233","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000233","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.434228Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":2,"action":"Accept the data use guidelines and download","detail":"The portal asks for acknowledgement and citation, not a data access request.","url":"https://pdc.cancer.gov/pdc/data-use-guidelines","requires":[],"est_time":"minutes to hours, by study size","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.434230Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":3,"action":"Resolve the study UUID, then fetch the file manifest","detail":"filesPerStudy keys on the study UUID, not on PDC000233: called with the pdc_study_id it returns the right number of rows with every column null. Resolve the UUID first and pass the terms acknowledgement.","url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","requires":[],"est_time":null,"cli_snippet":"python - <<'PY'\nimport requests\nAPI = \"https://proteomic.datacommons.cancer.gov/graphql\"\n\ndef gql(query, **variables):\n    r = requests.post(API, json={\"query\": query, \"variables\": variables}, timeout=180)\n    r.raise_for_status()\n    body = r.json()\n    if body.get(\"errors\"):\n        raise RuntimeError(body[\"errors\"][0][\"message\"])\n    return body[\"data\"]\n\nstudy = gql('query($id:String!){ study(pdc_study_id:$id acceptDUA:true){ study_id } }',\n            id=\"PDC000233\")[\"study\"][0]\nfiles = gql('query($sid:String!){ filesPerStudy(study_id:$sid acceptDUA:true)'\n            '{ file_id file_name file_size } }', sid=study[\"study_id\"])[\"filesPerStudy\"]\nprint(len(files), \"files\")\nPY","audience":"agent","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.434232Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]}],"analysis_examples":[],"agent_package":{"json_url":"/data/datasets/pdc-cptac-lscc-discovery-study.json","jsonld_url":"/data/jsonld/pdc-cptac-lscc-discovery-study.jsonld","croissant_url":"/data/croissant/pdc-cptac-lscc-discovery-study.json","instructions_url":"/data/agent/pdc-cptac-lscc-discovery-study.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"machine_only","reviewer":null,"reviewer_affiliation":null,"reviewed_at":null,"sections_reviewed":[],"open_questions":[],"notes":null},"verification":{"last_verified_at":null,"link_checks":[],"n_links_ok":0,"n_links_broken":0,"upstream_version_seen":null,"upstream_version_changed":false,"upstream_counts_seen":{},"upstream_drift":{},"notes":[]},"is_showcase":false,"completeness_score":32.1,"tags":["pdc","proteogenomics","rare-modality","acetylome","ubiquitylome"],"search_text":null}