Public API Documentation
The goal of the Proteomic Data Commons (PDC) project is to build a research resource for proteomics data that is interoperable, and leverages the investments made in other similar efforts for genomics and imaging data. The power of the individual datasets is enhanced by the addition of other supporting information and analysis using genomics, imaging and clinical data. The goal of the PDC, as one of the nodes in the CRDC ecosystem, is to demonstrate this value in an integrative resource, crossing multiple domains and enabling translational research for precision medicine.

The quickest way to get started with the GraphQL API is to use PDC GraphQL Explorer.

Important:

PDC studies can have multiple versions. While each version of study will have a UUID based unique study id, the PDC study ID (e.g., PDC000121) will always remain the same. By default, all the APIs will return the data related to the latest version. The APIs show the following behavior,

  • In order to understand the available versions, we strongly recommend you to first visit PDC portal or call the studyCatalog API. The studyCatalog API will provide a list of studies along with all their versions, version number and version status.
  • When calling an API with PDC study ID (e.g., PDC000121) as input parameter, it will return data for the latest version.
  • When calling an API with UUID based study ID (e.g., be2883cb-57b8-11e8-b07a-00a098d917f8) as input parameter, it will return data for the specific version.
      • Show samples

        Returns case details.

        Fields:

        • case_id
        • case_submitter_id
        • project_id
        • project_submitter_id
        • disease_type
        • primary_site
        • externalReferences { external_reference_id reference_resource_shortname reference_resource_name reference_entity_location }
        Click on the Try button to issue a test call to get the first ten cases (you can call the API without any parameters to get all 4500+ cases ):

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "allCases": [
              {
                "case_id": "327f8188-0a5d-11eb-bc0e-0aad30af8a83",
                "case_submitter_id": "05BR016",
                "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490",
                "project_submitter_id": "CPTAC-2",
                "disease_type": "Breast Invasive Carcinoma",
                "primary_site": "Breast",
                "externalReferences": [
                  {
                    "external_reference_id": "152f9e71-a437-4a4b-8c58-3ffcda41904b",
                    "reference_resource_shortname": "GDC",
                    "reference_resource_name": "Genomic Data Commons",
                    "reference_entity_location": "https://portal.gdc.cancer.gov/cases/152f9e71-a437-4a4b-8c58-3ffcda41904b"
                  }
                ]
              }
            ]
          }
        }
        {} allCases
        dataallCasesDef(optional)
        {} allCasesDef
        allCasesarray[allCasesDescription](optional)
        {} allCasesDescription
        case_idstring(optional)
        case_submitter_idstring(optional)
        project_idstring(optional)
        project_submitter_idstring(optional)
        disease_typestring(optional)
        primary_sitestring(optional)
        externalReferencesarray[ExternalReferencesAllCases](optional)
        {} ExternalReferencesAllCases
        external_reference_idstring(optional)
        reference_resource_shortnamestring(optional)
        reference_resource_namestring(optional)
        reference_entity_locationstring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • experiment_type (example: Label Free)
        • tissue_or_organ_of_origin (example: Cheek mucosa)
        • disease_type (example: Clear Cell Renal Cell Carcinoma)
        Returns a list of experiment types

        Fields:
        • experiment_type: Name of experiment type
        • tissue_or_organ_of_origin: Text term that describes the anatomic site of the tumor or disease
        • disease_type
        A test call can be issued with the following parameters:

        Parameters

        experiment_type
        string

        Experiment Type, example: Label Free

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "allExperimentTypes": [
              {
                "experiment_type": "Label Free",
                "tissue_or_organ_of_origin": "Kidney, NOS",
                "disease_type": "Clear Cell Renal Cell Carcinoma"
              }
            ]
          }
        }
        {} allExperiments
        dataallExperimentsDef(optional)
        {} allExperimentsDef
        allExperimentTypesarray[Experiment](optional)
        {} Experiment
        experiment_typestring(optional)
        tissue_or_organ_of_originstring(optional)
        disease_typestring(optional)
      • Show samples

        Returns a list of cases and a pagination record

        Fields:

        • total
        • cases
        • pagination
        A test call can be issued with the following parameters:

        Parameters

        offset
        integer

        Offset of records, example : 0

        limit
        integer

        Limit of records, example: 10

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "getPaginatedCases": {
              "total": 977,
              "cases": [
                {
                  "case_submitter_id": "05BR016",
                  "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490",
                  "project_submitter_id": "CPTAC-2",
                  "disease_type": "Breast Invasive Carcinoma"
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} getPaginatedCases
        datagetPaginatedCasesDef(optional)
        {} getPaginatedCasesDef
        getPaginatedCasesgetPaginatedCasesDesc(optional)
        {} getPaginatedCasesDesc
        totalnumber(optional)
        casesarray[allCasesDesc](optional)
        paginationPagination(optional)
        {} allCasesDesc
        case_submitter_idstring(optional)
        project_idstring(optional)
        project_submitter_idstring(optional)
        disease_typestring(optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000431)
        • study_name (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • offset (required for pagination, example: 0)
        • limit (required for pagination, example: 10)
        Returns cases/demographics per study
        It may take a long time to execute because of the huge volume of data.

        Fields:
        • total
        • caseDemographicsPerStudy
        • pagination
        A test call can be issued with the following parameters:

        Parameters

        study_id
        string

        Study ID, example: b93bb1e9-57b8-11e8-b07a-00a098d917f8

        offset
        integer

        Offset of records, example: 0

        limit
        integer

        Limit of records, example: 10

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "paginatedCaseDemographicsPerStudy": {
              "total": 93,
              "caseDemographicsPerStudy": [
                {
                  "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490",
                  "case_submitter_id": "C3N-00386",
                  "disease_type": "Uterine Corpus Endometrial Carcinoma",
                  "primary_site": "Uterus, NOS",
                  "demographics": [
                    {
                      "demographic_id": "848b480c-0f56-11e9-a064-0a9c39d33490",
                      "ethnicity": "Not Reported",
                      "gender": "Female",
                      "demographic_submitter_id": "C3N-00386-DEMO",
                      "race": "Not Reported",
                      "cause_of_death": "Not Reported",
                      "days_to_birth": "-16190",
                      "days_to_death": "0",
                      "vital_status": "Alive",
                      "year_of_birth": "1972",
                      "year_of_death": "0",
                      "age_at_index": "50",
                      "premature_at_birth": "Yes",
                      "weeks_gestation_at_birth": "6",
                      "age_is_obfuscated": "true",
                      "cause_of_death_source": "Autopsy",
                      "occupation_duration_years": "30",
                      "country_of_residence_at_enrollment": "Afghanistan"
                    }
                  ]
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} paginatedCaseDemographicsPerStudy
        datapaginatedCaseDemographicsPerStudyDef(optional)
        {} paginatedCaseDemographicsPerStudyDef
        paginatedCaseDemographicsPerStudypaginatedCaseDemographicsPerStudyDesc(optional)
        {} paginatedCaseDemographicsPerStudyDesc
        totalnumber(optional)
        caseDemographicsPerStudyarray[paginatedCaseDemographics](optional)
        paginationPagination(optional)
        {} paginatedCaseDemographics
        case_idstring(optional)
        case_submitter_idstring(optional)
        disease_typestring(optional)
        primary_sitestring(optional)
        demographicsarray[Demographic](optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
        {} Demographic
        demographic_idstring(optional)
        ethnicitystring(optional)
        genderstring(optional)
        demographic_submitter_idstring(optional)
        racestring(optional)
        cause_of_deathstring(optional)
        days_to_birthinteger(optional)
        days_to_deathinteger(optional)
        vital_statusstring(optional)
        year_of_birthinteger(optional)
        year_of_deathinteger(optional)
        age_at_indexinteger(optional)
        premature_at_birthstring(optional)
        weeks_gestation_at_birthinteger(optional)
        age_is_obfuscatedboolean(optional)
        cause_of_death_sourcestring(optional)
        occupation_duration_yearsinteger(optional)
        country_of_residence_at_enrollmentstring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000431)
        • study_name (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • offset (required for pagination, example: 0)
        • limit (required for pagination, example: 10)
        Returns cases/exposures per study.
        It may take a long time to execute because of the huge volume of data.

        Fields:
        • total
        • caseExposuresPerStudy
        • pagination
        A test call can be issued with the following parameters:

        Parameters

        study_submitter_id
        string

        Study Submitter ID, example: CPTAC UCEC Discovery Study - Acetylome

        offset
        integer

        Offset of records, example: 0

        limit
        integer

        Limit of records, example: 10

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "paginatedCaseExposuresPerStudy": {
              "total": 93,
              "caseExposuresPerStudy": [
                {
                  "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490",
                  "case_submitter_id": "C3N-00386",
                  "disease_type": "Uterine Corpus Endometrial Carcinoma",
                  "primary_site": "Uterus, NOS",
                  "exposures": [
                    {
                      "exposure_id": "848b480c-0f56-11e9-a064-0a9c39d33490",
                      "exposure_submitter_id": "C3N-00386-EX",
                      "alcohol_days_per_week": "3",
                      "alcohol_drinks_per_day": "2",
                      "alcohol_history": "Yes",
                      "alcohol_intensity": "Lifelong Non-Drinker",
                      "asbestos_exposure": "Not Reported",
                      "cigarettes_per_day": "5",
                      "coal_dust_exposure": "Not Reported",
                      "environmental_tobacco_smoke_exposure": "Not Reported",
                      "pack_years_smoked": "52",
                      "radon_exposure": "Not Reported",
                      "respirable_crystalline_silica_exposure": "Not Reported",
                      "smoking_frequency": "Not Reported",
                      "time_between_waking_and_first_smoke": "Not Reported",
                      "tobacco_smoking_onset_year": "1972",
                      "tobacco_smoking_quit_year": "1992",
                      "tobacco_smoking_status": "Not Reported",
                      "type_of_smoke_exposure": "Smoke exposure, NOS",
                      "type_of_tobacco_used": "pipe",
                      "years_smoked": "20",
                      "age_at_onset": "45",
                      "alcohol_type": "Liquor",
                      "exposure_duration": "Six Weeks or More",
                      "exposure_duration_years": "15",
                      "exposure_type": "Marijuana",
                      "marijuana_use_per_week": "3.5",
                      "parent_with_radiation_exposure": "Not Reported",
                      "secondhand_smoke_as_child": "Unknown",
                      "smokeless_tobacco_quit_age": "48",
                      "tobacco_use_per_day": "7.5"
                    }
                  ]
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} paginatedCaseExposuresPerStudy
        datapaginatedCaseExposuresPerStudyDef(optional)
        {} paginatedCaseExposuresPerStudyDef
        paginatedCaseExposuresPerStudypaginatedCaseExposuresPerStudyDesc(optional)
        {} paginatedCaseExposuresPerStudyDesc
        totalnumber(optional)
        caseExposuresPerStudyarray[paginatedCaseExposures](optional)
        paginationPagination(optional)
        {} paginatedCaseExposures
        case_idstring(optional)
        case_submitter_idstring(optional)
        disease_typestring(optional)
        primary_sitestring(optional)
        exposuresarray[Exposure](optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
        {} Exposure
        exposure_idstring(optional)
        exposure_submitter_idstring(optional)
        alcohol_days_per_weekinteger(optional)
        alcohol_drinks_per_dayinteger(optional)
        alcohol_historystring(optional)
        alcohol_intensitystring(optional)
        asbestos_exposurestring(optional)
        cigarettes_per_dayinteger(optional)
        coal_dust_exposurestring(optional)
        environmental_tobacco_smoke_exposurestring(optional)
        pack_years_smokedinteger(optional)
        radon_exposurestring(optional)
        respirable_crystalline_silica_exposurestring(optional)
        smoking_frequencystring(optional)
        time_between_waking_and_first_smokestring(optional)
        tobacco_smoking_onset_yearinteger(optional)
        tobacco_smoking_quit_yearinteger(optional)
        tobacco_smoking_statusstring(optional)
        type_of_smoke_exposurestring(optional)
        type_of_tobacco_usedstring(optional)
        years_smokedinteger(optional)
        age_at_onsetinteger(optional)
        alcohol_typestring(optional)
        exposure_durationstring(optional)
        exposure_duration_yearsinteger(optional)
        exposure_typestring(optional)
        marijuana_use_per_weeknumber(optional)
        parent_with_radiation_exposurestring(optional)
        secondhand_smoke_as_childstring(optional)
        smokeless_tobacco_quit_ageinteger(optional)
        tobacco_use_per_daynumber(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 8961afcf-05de-4b7c-b471-ca1a4887ed36)
        • study_submitter_id (example: APOLLO LUAD - Phosphoproteome - FeNTA)
        • pdc_study_id (example: PDC000436)
        • study_name (example: APOLLO LUAD - Phosphoproteome - FeNTA)
        • offset (required for pagination, example: 0)
        • limit (required for pagination, example: 10)
        Returns cases/treatments per study.
        It may take a long time to execute because of the huge volume of data.

        Fields:
        • total
        • caseTreatmentsPerStudy
        • pagination
        A test call can be issued with the following parameters:

        Parameters

        pdc_study_id
        string

        PDC Study ID, example: PDC000436

        offset
        integer

        Offset of records, example: 0

        limit
        integer

        Limit of records, example: 10

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "paginatedCaseTreatmentsPerStudy": {
              "total": 230,
              "caseTreatmentsPerStudy": [
                {
                  "case_id": "e0d672dc-b42b-4721-82bd-deae88280c69",
                  "case_submitter_id": "AP-27JZ",
                  "disease_type": "Lung Adenocarcinoma",
                  "primary_site": "Bronchus and lung",
                  "treatments": [
                    {
                      "treatment_id": "a2518568-1adc-43fe-852f-049ad21ec2df",
                      "treatment_submitter_id": "AP-27JZ-TR",
                      "days_to_treatment_end": " ",
                      "days_to_treatment_start": " ",
                      "initial_disease_status": " ",
                      "regimen_or_line_of_therapy": " ",
                      "therapeutic_agents": " ",
                      "treatment_anatomic_site": " ",
                      "treatment_effect": " ",
                      "treatment_intent_type": "Adjuvant",
                      "treatment_or_therapy": " ",
                      "treatment_outcome": " ",
                      "treatment_type": "Radiation Therapy, NOS",
                      "chemo_concurrent_to_radiation": " ",
                      "number_of_cycles": " ",
                      "reason_treatment_ended": " ",
                      "route_of_administration": " ",
                      "treatment_arm": " ",
                      "treatment_dose": " ",
                      "treatment_dose_units": " ",
                      "treatment_effect_indicator": " ",
                      "treatment_frequency": " "
                    }
                  ]
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} paginatedCaseTreatmentsPerStudy
        datapaginatedCaseTreatmentsPerStudyDef(optional)
        {} paginatedCaseTreatmentsPerStudyDef
        paginatedCaseTreatmentsPerStudypaginatedCaseTreatmentsPerStudyDesc(optional)
        {} paginatedCaseTreatmentsPerStudyDesc
        totalnumber(optional)
        caseTreatmentsPerStudyarray[paginatedCaseTreatments](optional)
        paginationPagination(optional)
        {} paginatedCaseTreatments
        case_idstring(optional)
        case_submitter_idstring(optional)
        disease_typestring(optional)
        primary_sitestring(optional)
        treatmentsarray[Treatment](optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
        {} Treatment
        treatment_idstring(optional)
        treatment_submitter_idstring(optional)
        days_to_treatment_endinteger(optional)
        days_to_treatment_startinteger(optional)
        initial_disease_statusstring(optional)
        regimen_or_line_of_therapystring(optional)
        therapeutic_agentsstring(optional)
        treatment_anatomic_sitestring(optional)
        treatment_effectstring(optional)
        treatment_intent_typestring(optional)
        treatment_or_therapystring(optional)
        treatment_outcomestring(optional)
        treatment_typestring(optional)
        chemo_concurrent_to_radiationstring(optional)
        number_of_cyclesinteger(optional)
        reason_treatment_endedstring(optional)
        route_of_administrationstring(optional)
        treatment_armstring(optional)
        treatment_doseinteger(optional)
        treatment_dose_unitsstring(optional)
        treatment_effect_indicatorstring(optional)
        treatment_frequencystring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • program_name (example: Clinical Proteomic Tumor Analysis Consortium)
        • project_name (example: CPTAC3 Discovery and Confirmatory)
        • program_submitter_id (example: Clinical Proteomic Tumor Analysis Consortium)
        • project_submitter_id (example: CPTAC3 Discovery and Confirmatory)
        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000431)
        • study_name (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • offset (required for pagination, example: 0)
        • limit (required for pagination, example: 10)
        Returns a list of cases, samples amd aliquot records.

        Fields:
        • total
        • casesSamplesAliquots
        • pagination
        A test call can be issued with the following parameters:

        Parameters

        pdc_study_id
        integer

        PDC Study ID, example : PDC000226

        offset
        integer

        Offset of records, example : 0

        limit
        integer

        Limit of records, example: 10

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "paginatedCasesSamplesAliquots": {
              "total": 958,
              "casesSamplesAliquots": [
                {
                  "case_id": "a023e964-118a-11e9-afb9-0a9c39d33490",
                  "case_submitter_id": "C3N-00386",
                  "days_to_lost_to_followup": 0,
                  "disease_type": "Uterine Corpus Endometrial Carcinoma",
                  "index_date": "Diagnosis",
                  "lost_to_followup": "string",
                  "primary_site": "Uterus, NOS",
                  "samples": [
                    {
                      "sample_id": "99a4bcef-1259-11e9-afb9-0a9c39d33490",
                      "sample_submitter_id": "C3N-00386-02",
                      "sample_type": "Primary Tumor",
                      "sample_type_id": "null",
                      "gdc_sample_id": "null",
                      "gdc_project_id": "null",
                      "biospecimen_anatomic_site": "Not Reported",
                      "composition": "Solid Tissue",
                      "current_weight": "0",
                      "days_to_collection": "0",
                      "days_to_sample_procurement": "0",
                      "diagnosis_pathologically_confirmed": "Not Reported",
                      "freezing_method": "LN2",
                      "initial_weight": "400",
                      "intermediate_dimension": "null",
                      "longest_dimension": "null",
                      "method_of_sample_procurement": "Not Reported",
                      "pathology_report_uuid": "null",
                      "preservation_method": "Snap Frozen",
                      "shortest_dimension": "null",
                      "time_between_clamping_and_freezing": "0",
                      "time_between_excision_and_freezing": "11",
                      "tissue_type": "Tumor",
                      "tumor_code": "null",
                      "tumor_code_id": "null",
                      "tumor_descriptor": "Not Reported",
                      "biospecimen_laterality": "Bilateral",
                      "catalog_reference": "Not Reported",
                      "distance_normal_to_tumor": "Adjacent (< or = 2cm)",
                      "distributor_reference": "Not Reported",
                      "growth_rate": "1",
                      "passage_count": "2",
                      "sample_ordinal": "3",
                      "tissue_collection_type": "Prospective",
                      "diagnoses": [
                        {
                          "diagnosis_id": "f748299b-0f5a-11e9-a064-0a9c39d33490",
                          "diagnosis_submitter_id": "C3N-00386-DIAG",
                          "annotation": "The sample 7316-2901 is associated with this clinical record."
                        }
                      ],
                      "aliquots": [
                        {
                          "aliquot_id": "141959ca-6424-11e8-bcf1-0a2705229b82",
                          "aliquot_submitter_id": "3f957017-d081-45f4-b458-ec3f8d_D2",
                          "analyte_type": "Protein",
                          "aliquot_run_metadata": [
                            {
                              "aliquot_run_metadata_id": "1661cee5-5731-11e8-b664-00a098d917f8",
                              "label": "itraq_116",
                              "experiment_number": "13",
                              "fraction": "24-Jan",
                              "replicate_number": "1",
                              "date": "2013-02-28",
                              "alias": "B1S6",
                              "analyte": "Proteome"
                            }
                          ]
                        }
                      ]
                    }
                  ]
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} paginatedCasesSamplesAliquots
        datapaginatedCasesSamplesAliquotsDef(optional)
        {} paginatedCasesSamplesAliquotsDef
        paginatedCasesSamplesAliquotscasesSamplesAliquotsDesc(optional)
        {} casesSamplesAliquotsDesc
        totalnumber(optional)
        casesSamplesAliquotsarray[Case](optional)
        paginationPagination(optional)
        {} Case
        case_idstring(optional)
        case_submitter_idstring(optional)
        days_to_lost_to_followupinteger(optional)
        disease_typestring(optional)
        index_datestring(optional)
        lost_to_followupstring(optional)
        primary_sitestring(optional)
        samplesarray[Sample](optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
        {} Sample
        sample_idstring(optional)
        sample_submitter_idstring(optional)
        sample_typestring(optional)
        sample_type_idstring(optional)
        gdc_sample_idstring(optional)
        gdc_project_idstring(optional)
        biospecimen_anatomic_sitestring(optional)
        compositionstring(optional)
        current_weightstring(optional)
        days_to_collectionstring(optional)
        days_to_sample_procurementstring(optional)
        diagnosis_pathologically_confirmedstring(optional)
        freezing_methodstring(optional)
        initial_weightstring(optional)
        intermediate_dimensionstring(optional)
        longest_dimensionstring(optional)
        method_of_sample_procurementstring(optional)
        pathology_report_uuidstring(optional)
        preservation_methodstring(optional)
        shortest_dimensionstring(optional)
        time_between_clamping_and_freezingstring(optional)
        time_between_excision_and_freezingstring(optional)
        tissue_typestring(optional)
        tumor_codestring(optional)
        tumor_code_idstring(optional)
        tumor_descriptorstring(optional)
        biospecimen_lateralitystring(optional)
        catalog_referencestring(optional)
        distance_normal_to_tumorstring(optional)
        distributor_referencestring(optional)
        growth_rateinteger(optional)
        passage_countinteger(optional)
        sample_ordinalinteger(optional)
        tissue_collection_typestring(optional)
        diagnosesarray[DiagnosisRef](optional)
        aliquotsarray[Aliquot](optional)
        {} DiagnosisRef
        diagnosis_idstring(optional)
        diagnosis_submitter_idstring(optional)
        annotationstring(optional)
        {} Aliquot
        aliquot_idstring
        aliquot_submitter_idstring
        analyte_typestring(optional)
        aliquot_run_metadataarray[aliquotRunMetaDataForPaginated](optional)
        {} aliquotRunMetaDataForPaginated
        aliquot_run_metadata_idstring(optional)
        labelstring(optional)
        experiment_numberstring(optional)
        fractionstring(optional)
        replicate_numberstring(optional)
        datestring(optional)
        aliasstring(optional)
        analytestring(optional)
      • Show samples

        Returns all available programs.

        Fields:

        • program_id
        • program_submitter_id
        • name
        • projects
        Click on the Try button to issue a test call:

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "allPrograms": [
              {
                "program_id": "10251935-5540-11e8-b664-00a098d917f8",
                "program_submitter_id": "Clinical Proteomic Tumor Analysis Consortium",
                "name": "Clinical Proteomic Tumor Analysis Consortium",
                "projects": [
                  {
                    "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490",
                    "project_submitter_id": "CPTAC3-Discovery",
                    "name": "CPTAC3-Discovery",
                    "studies": [
                      {
                        "pdc_study_id": "PDC000206",
                        "study_id": "0ea91a54-1798-11ea-9bfa-0a42f3c845fe",
                        "study_submitter_id": "CPTAC GBM Discovery Study - CompRef Phosphoproteome",
                        "submitter_id_name": "CPTAC GBM Discovery Study - CompRef Phosphoproteome",
                        "analytical_fraction": "Phosphoproteome",
                        "study_name": "CPTAC LSCC Discovery Study - Phosphoproteome",
                        "disease_types": "[Lung Adenocarcinoma, Other]",
                        "primary_sites": "[Lung, Bronchus and lung]",
                        "experiment_type": "TMT11",
                        "acquisition_type": "DDA"
                      }
                    ]
                  }
                ]
              }
            ]
          }
        }
        {} allPrograms
        dataallProgramsDef(optional)
        {} allProgramsDef
        allProgramsarray[allProgramsDesc](optional)
        {} allProgramsDesc
        program_idstring(optional)
        program_submitter_idstring(optional)
        namestring(optional)
        projectsarray[allProgramsProject](optional)
        {} allProgramsProject
        project_idstringPK
        project_submitter_idstring(optional)
        namestring(optional)
        studiesarray[allProgramsStudy](optional)
        {} allProgramsStudy
        pdc_study_idstring(optional)
        study_idstringPK
        study_submitter_idstring(optional)
        submitter_id_namestring(optional)
        analytical_fractionstring(optional)
        study_namestring(optional)
        disease_typesstring(optional)
        primary_sitesstring(optional)
        experiment_typestring(optional)
        acquisition_typestring(optional)
      • Show samples

        Input Parameters:

        • program_id (example: c3408a52-f1e8-11e9-9a07-0a80fada099c)
        • program_submitter_id (example: Clinical Proteomic Tumor Analysis Consortium)
        Returns a single program and its projects.

        Fields:

        • program_id
        • program_submitter_id
        • name
        • projects
        A test call can be issued with the following parameter:

        Parameters

        program_submitter_id
        string

        Program Submitter ID, example: Clinical Proteomic Tumor Analysis Consortium

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "program": {
              "program_submitter_id": "CPTAC",
              "projects": [
                {
                  "program_id": "10251935-5540-11e8-b664-00a098d917f8",
                  "program_submitter_id": "Clinical Proteomic Tumor Analysis Consortium",
                  "name": "Clinical Proteomic Tumor Analysis Consortium",
                  "projects": [
                    {
                      "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490",
                      "project_submitter_id": "CPTAC3-Discovery",
                      "name": "CPTAC3-Discovery",
                      "studies": [
                        {
                          "pdc_study_id": "PDC000206",
                          "study_id": "0ea91a54-1798-11ea-9bfa-0a42f3c845fe",
                          "study_submitter_id": "CPTAC GBM Discovery Study - CompRef Phosphoproteome",
                          "submitter_id_name": "CPTAC GBM Discovery Study - CompRef Phosphoproteome",
                          "analytical_fraction": "Phosphoproteome",
                          "study_name": "CPTAC LSCC Discovery Study - Phosphoproteome",
                          "disease_types": "[Lung Adenocarcinoma, Other]",
                          "primary_sites": "[Lung, Bronchus and lung]",
                          "experiment_type": "TMT11",
                          "acquisition_type": "DDA"
                        }
                      ]
                    }
                  ]
                }
              ]
            }
          }
        }
        {} findProgram
        datafindProgramObj(optional)
        {} findProgramObj
        programfindProgramDef(optional)
        {} findProgramDef
        program_submitter_idstring(optional)
        projectsarray[allProgramsDesc](optional)
        {} allProgramsDesc
        program_idstring(optional)
        program_submitter_idstring(optional)
        namestring(optional)
        projectsarray[allProgramsProject](optional)
        {} allProgramsProject
        project_idstringPK
        project_submitter_idstring(optional)
        namestring(optional)
        studiesarray[allProgramsStudy](optional)
        {} allProgramsStudy
        pdc_study_idstring(optional)
        study_idstringPK
        study_submitter_idstring(optional)
        submitter_id_namestring(optional)
        analytical_fractionstring(optional)
        study_namestring(optional)
        disease_typesstring(optional)
        primary_sitesstring(optional)
        experiment_typestring(optional)
        acquisition_typestring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • disease_type (example: Lung Adenocarcinoma)
        • instrument_model (example: Q Exactive)
        • analytical_fraction (example: Phosphoproteome)
        • experiment_type (example: iTRAQ4)
        Returns a hierarchy of programs/projects/studies.

        Fields:
        • program_id
        • program_submitter_id
        • name
        • projects {project_id project_submitter_id name}
        • studies {pdc_study_id study_id study_submitter_id submitter_id_name analytical_fraction study_name disease_types primary_sites experiment_type acquisition_type}
        A test call can be issued with the following parameter:

        Parameters

        disease_type
        string

        Disease Type Example: Lung Adenocarcinoma

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "programsProjectsStudies": [
              {
                "program_id": "10251935-5540-11e8-b664-00a098d917f8",
                "program_submitter_id": "Clinical Proteomic Tumor Analysis Consortium",
                "name": "Clinical Proteomic Tumor Analysis Consortium",
                "projects": [
                  {
                    "project_id": "PJ-CPTAC3",
                    "project_submitter_id": "PJ-CPTAC3",
                    "name": "PJ-CPTAC3",
                    "studies": [
                      {
                        "pdc_study_id": "PDC000125",
                        "study_id": "c935c587-0cd1-11e9-a064-0a9c39d33490",
                        "submitter_id_name": "CPTAC UCEC Discovery Study - Proteome",
                        "study_submitter_id": "S043-1",
                        "analytical_fraction": "Proteome",
                        "study_name": "CPTAC LSCC Discovery Study - Phosphoproteome",
                        "disease_types": "[Lung Adenocarcinoma, Other]",
                        "primary_sites": "[Lung, Bronchus and lung]",
                        "experiment_type": "TMT10",
                        "acquisition_type": "DDA"
                      }
                    ]
                  }
                ]
              }
            ]
          }
        }
        {} programsProjectsStudies
        dataprogramsProjectsStudiesDef(optional)
        {} programsProjectsStudiesDef
        programsProjectsStudiesarray[programsProjectsStudiesDesc](optional)
        {} programsProjectsStudiesDesc
        program_idstring(optional)
        program_submitter_idstring(optional)
        namestring(optional)
        projectsarray[programsProjectsStudiesDefforProj](optional)
        {} programsProjectsStudiesDefforProj
        project_idstring(optional)
        project_submitter_idstring(optional)
        namestring(optional)
        studiesarray[programsProjectsStudiesDefforStudies](optional)
        {} programsProjectsStudiesDefforStudies
        pdc_study_idstring(optional)
        study_idstring(optional)
        submitter_id_namestring(optional)
        study_submitter_idstring(optional)
        analytical_fractionstring(optional)
        study_namestring(optional)
        disease_typesstring(optional)
        primary_sitesstring(optional)
        experiment_typestring(optional)
        acquisition_typestring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • gene_name (example: MYBBP1A)
        • dataset_alias (example: FFPE_Discovery_Phospho_TMT_Gr12)
        Returns the aliquot spectral counts

        Fields:
        • gene_id
        • gene_name
        • NCBI_gene_id
        • authority
        • description
        • organism
        • chromosome
        • locus
        • proteins
        • assays
        • spectral_counts
        A test call can be issued with the following parameters (it may return slowly or even time out the first time due to the data volume. However, the result is cached and will be returned promptly if you try with the same parameters again):

        Parameters

        gene_name
        string

        Gene Name, example: MYBBP1A

        dataset_alias
        string

        Dataset alias, example: FFPE_Discovery_Phospho_TMT_Gr12

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "aliquotSpectralCount": {
              "gene_id": "f6ba4bc5-b814-11e8-907f-0a2705229b82",
              "gene_name": "A1BG",
              "NCBI_gene_id": "1",
              "authority": "HGNC:5",
              "description": "alpha-1-B glycoprotein",
              "organism": "Homo sapiens",
              "chromosome": "19",
              "locus": "19q13.43",
              "proteins": "M0R009;NP_570602.2;P04217;P04217-2",
              "assays": "non-CPTAC-1064",
              "spectral_counts": [
                {
                  "project_submitter_id": "CPTAC-TCGA",
                  "project_id": "48653303-5546-11e8-b664-00a098d917f8",
                  "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329",
                  "spectral_count": "11",
                  "distinct_peptide": "5",
                  "unshared_peptide": "5",
                  "study_id": "bb67ec40-57b8-11e8-b07a-00a098d917f8",
                  "study_submitter_id": "S015-2",
                  "pdc_study_id": "PDC000174"
                }
              ]
            }
          }
        }
        {} aliquotSpectralCount
        dataaliquotSpectralCountDef(optional)
        {} aliquotSpectralCountDef
        aliquotSpectralCountaliquotSpectralCountDesc(optional)
        {} aliquotSpectralCountDesc
        gene_idstring(optional)
        gene_namestring(optional)
        NCBI_gene_idnumber(optional)
        authoritystring(optional)
        descriptionstring(optional)
        organismstring(optional)
        chromosomestring(optional)
        locusstring(optional)
        proteinsstring(optional)
        assaysstring(optional)
        spectral_countsarray[spectralCountsDesc](optional)
        {} spectralCountsDesc
        project_submitter_idstring(optional)
        project_idstring(optional)
        plexstring(optional)
        spectral_countnumber(optional)
        distinct_peptidenumber(optional)
        unshared_peptidenumber(optional)
        study_idstring(optional)
        study_submitter_idnumber(optional)
        pdc_study_idnumber(optional)
      • Show samples

        Input Parameter:

        • gene_name (example: A1BG)
        Returns the gene spectral counts

        Fields:
        • gene_id
        • gene_name
        • NCBI_gene_id
        • authority
        • description
        • organism
        • chromosome
        • locus
        • proteins
        • assays
        • spectral_counts
        A test call can be issued with the following parameter (it may return slowly or even time out the first time due to the data volume. However, the result is cached and will be returned promptly if you try with the same parameter again):

        Parameters

        gene_name
        string

        Gene Name, example: A1BG

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "geneSpectralCount": {
              "gene_id": "f6ba4bc5-b814-11e8-907f-0a2705229b82",
              "gene_name": "A1BG",
              "NCBI_gene_id": "1",
              "authority": "HGNC:5",
              "description": "alpha-1-B glycoprotein",
              "organism": "Homo sapiens",
              "chromosome": "19",
              "locus": "19q13.43",
              "proteins": "M0R009;NP_570602.2;P04217;P04217-2",
              "assays": "non-CPTAC-1064",
              "spectral_counts": [
                {
                  "project_submitter_id": "CPTAC-TCGA",
                  "project_id": "48653303-5546-11e8-b664-00a098d917f8",
                  "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329",
                  "spectral_count": "11",
                  "distinct_peptide": "5",
                  "unshared_peptide": "5",
                  "study_id": "bb67ec40-57b8-11e8-b07a-00a098d917f8",
                  "study_submitter_id": "S015-2",
                  "pdc_study_id": "PDC000174"
                }
              ]
            }
          }
        }
        {} geneSpectralCount
        datageneSpectralCountDef(optional)
        {} geneSpectralCountDef
        geneSpectralCountaliquotSpectralCountDesc(optional)
        {} aliquotSpectralCountDesc
        gene_idstring(optional)
        gene_namestring(optional)
        NCBI_gene_idnumber(optional)
        authoritystring(optional)
        descriptionstring(optional)
        organismstring(optional)
        chromosomestring(optional)
        locusstring(optional)
        proteinsstring(optional)
        assaysstring(optional)
        spectral_countsarray[spectralCountsDesc](optional)
        {} spectralCountsDesc
        project_submitter_idstring(optional)
        project_idstring(optional)
        plexstring(optional)
        spectral_countnumber(optional)
        distinct_peptidenumber(optional)
        unshared_peptidenumber(optional)
        study_idstring(optional)
        study_submitter_idnumber(optional)
        pdc_study_idnumber(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • gene_name (example: A1BG)
        Returns a list of genes and a pagination record

        Fields:
        • total
        • genesProper
        • pagination
        A test call can be issued with the following parameters:

        Parameters

        gene_name
        string

        Gene Name, example: A1BG

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "getPaginatedGenes": {
              "total": 2,
              "genesProper": [
                {
                  "gene_id": "f6baad59-b814-11e8-907f-0a2705229b82",
                  "gene_name": "A2ML1",
                  "NCBI_gene_id": "144568",
                  "authority": "HGNC:23336",
                  "description": "alpha-2-macroglobulin like 1",
                  "organism": "Homo sapiens",
                  "chromosome": "12",
                  "locus": "12p13.31",
                  "proteins": "A8K2U0;A8K2U0-2;F5GXP1;F5GYG7;H0YGG5;H0YH14;NP_001269353.1;NP_653271.2;XP_011518868.1;XP_011518869.1;XP_016874357.1;XP_016874358.1;XP_016874359.1",
                  "assays": "non-CPTAC-1064"
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} getPaginatedGenes
        datagetPaginatedGenesDef(optional)
        {} getPaginatedGenesDef
        getPaginatedGenesgetPaginatedGenesDesc(optional)
        {} getPaginatedGenesDesc
        totalnumber(optional)
        genesProperarray[genesProper](optional)
        paginationPagination(optional)
        {} genesProper
        gene_idstring(optional)
        gene_namestring(optional)
        NCBI_gene_idnumber(optional)
        authoritystring(optional)
        descriptionstring(optional)
        organismstring(optional)
        chromosomestring(optional)
        locusstring(optional)
        proteinsstring(optional)
        assaysstring(optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • disease_type (example: Breast Invasive Carcinoma)
        • tissue_or_organ_of_origin (example: Breast)
        • project_submitter_id (example: CPTAC-2)
        • project_id (example: 48653303-5546-11e8-b664-00a098d917f8)
        Returns a list of disease types.

        Fields:
        • disease_type
        • project_id
        • project_submitter_id
        • cases_count
        • tissue_or_organ_of_origin
        A test call can be issued by clicking on TRY:

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "diseasesAvailable": [
              {
                "disease_type": "Breast Invasive Carcinoma",
                "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490",
                "project_submitter_id": "CPTAC-2",
                "cases_count": "116",
                "tissue_or_organ_of_origin": "Breast, NOS"
              }
            ]
          }
        }
        {} diseasesAvailable
        datadiseasesAvailableDef(optional)
        {} diseasesAvailableDef
        diseasesAvailablearray[diseasesAvailableDesc](optional)
        {} diseasesAvailableDesc
        disease_typestring(optional)
        project_idstring(optional)
        project_submitter_idstring(optional)
        cases_countstring(optional)
        tissue_or_organ_of_originnumber(optional)
      • Show samples

        Input Parameters:

        • project_submitter_id (example: CPTAC-2)
        • project_id (example: 48653303-5546-11e8-b664-00a098d917f8)
        Returns a list of disease types.

        Fields:
        • project_id
        • project_submitter_id
        • experiment_type
        • analytical_fraction
        • cases {disease_type count}
        A test call can be issued by clicking on TRY:

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "diseaseTypesPerProject": [
              {
                "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490",
                "project_submitter_id": "Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study",
                "experiment_type": "TMT11",
                "analytical_fraction": "Proteome",
                "cases": [
                  {
                    "disease_type": "Clear Cell Renal Cell Carcinoma",
                    "count": 6
                  }
                ]
              }
            ]
          }
        }
        {} diseaseTypesPerProject
        datadiseaseTypesPerProjectDef(optional)
        {} diseaseTypesPerProjectDef
        diseaseTypesPerProjectarray[diseaseTypesPerProjectDesc](optional)
        {} diseaseTypesPerProjectDesc
        project_idstring(optional)
        project_submitter_idstring(optional)
        experiment_typenumber(optional)
        analytical_fractionstring(optional)
        casesarray[casesForDiseaseTypeDesc](optional)
        {} casesForDiseaseTypeDesc
        disease_typestring(optional)
        countnumber(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000431)
        • file_type (example: Proprietary)
        • data_category (example: Raw Mass Spectra)
        Returns all records with counts of files per study per file type.

        Fields:
        • study_id
        • pdc_study_id
        • study_submitter_id: ID of a study
        • file_type
        • files_count
        • data_category
        A test call can be issued with the following parameters:

        Parameters

        pdc_study_id
        string

        PDC Study ID, example: PDC000431

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "filesCountPerStudy": [
              {
                "study_id": "1c163e4c-e015-43e0-bd76-238eebd64e5a",
                "pdc_study_id": "PDC000206",
                "study_submitter_id": "CPTAC GBM Discovery Study - CompRef Phosphoproteome",
                "file_type": "Document",
                "files_count": 11,
                "data_category": "Other Metadata"
              }
            ]
          }
        }
        {} filesCountPerStudy
        datafilesCountPerStudyDef(optional)
        {} filesCountPerStudyDef
        filesCountPerStudyarray[filesCountPerStudyDesc](optional)
        {} filesCountPerStudyDesc
        study_idstring(optional)
        pdc_study_idstring(optional)
        study_submitter_idstring(optional)
        file_typenumber(optional)
        files_countnumber(optional)
        data_categorystring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • file_id (example: 00046804-1b57-11e9-9ac1-005056921935)
        • file_name (example: 20151104-P50-20ug-s35.mzML.gz)
        • file_submitter_id (example: 20190125_30ug_OCb5_T_p_s40.raw)
        • data_category (example: Raw Mass Spectra)
        • file_type (example: Proprietary)
        • file_format (example: vendor-specific)
        • offset (example: 0)
        • limit (example: 10 cannot exceed 25000)
        Returns a list of file metadata

        Fields:
        • file_id
        • file_name
        • file_size
        • md5sum
        • file_location
        • file_submitter_id
        • fraction_number
        • experiment_type
        • data_category
        • file_type
        • file_format
        • plex_or_dataset_name
        • analyte
        • instrument
        • study_run_metadata_submitter_id
        • study_run_metadata_id
        • aliquots
        A test call can be issued with the following parameters:

        Parameters

        offset
        integer

        Offset of records, example : 0

        limit
        integer

        Limit of records, example: 10

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "fileMetadata": [
              {
                "file_id": "00046804-1b57-11e9-9ac1-005056921935",
                "file_name": "06CPTAC_CCRCC_W_JHU_20171120_LUMOS_f09.mzid.gz",
                "file_size": "7290779",
                "md5sum": "e8d4417af70878bb1cf45f8a0fca9433",
                "file_location": "studies/127/PSM/mzid/06CPTAC_CCRCC_W_JHU_20171120_LUMOS_f09.mzid.gz",
                "file_submitter_id": "06CPTAC_CCRCC_W_JHU_20171120_LUMOS_f09.mzid.gz",
                "fraction_number": "9",
                "experiment_type": "TMT10",
                "data_category": "Peptide Spectral Matches",
                "file_type": "Open Standard",
                "file_format": "mzIdentML",
                "plex_or_dataset_name": "06CPTAC_CCRCC_Proteome_JHU_20171120",
                "analyte": "Proteome",
                "instrument": "Orbitrap Fusion Lumos",
                "study_run_metadata_submitter_id": "S044-1-9",
                "study_run_metadata_id": "f7fdea37-2074-11e9-b7f8-0a80fada099c",
                "aliquots": [
                  {
                    "aliquot_id": "4f9821f1-2053-11e9-b7f8-0a80fada099c",
                    "aliquot_submitter_id": "CPT0000790001",
                    "sample_id": "7e25284f-204c-11e9-b7f8-0a80fada099c",
                    "sample_submitter_id": "C3L-00097-06",
                    "case_id": "b76d3749-1fb8-11e9-b7f8-0a80fada099c",
                    "case_submitter_id": "C3L-00097"
                  }
                ]
              }
            ]
          }
        }
        {} fileMetadata
        datafileMetadataDef(optional)
        {} fileMetadataDef
        fileMetadataarray[fileMetadataDesc](optional)
        {} fileMetadataDesc
        file_idstring(optional)
        file_namestring(optional)
        file_sizestring(optional)
        md5sumstring(optional)
        file_locationstring(optional)
        file_submitter_idstring(optional)
        fraction_numberstring(optional)
        experiment_typestring(optional)
        data_categorystring(optional)
        file_typestring(optional)
        file_formatstring(optional)
        plex_or_dataset_namestring(optional)
        analytestring(optional)
        instrumentstring(optional)
        study_run_metadata_submitter_idstring(optional)
        study_run_metadata_idstring(optional)
        aliquotsarray[fileMetadataAliquotsDesc](optional)
        {} fileMetadataAliquotsDesc
        aliquot_idstring(optional)
        aliquot_submitter_idstring(optional)
        sample_idstring(optional)
        sample_submitter_idstring(optional)
        case_idstring(optional)
        case_submitter_idstring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000431)
        • file_type (example: Proprietary)
        • file_name (example: BL20161004_BI_FM_Medullo_pY_Plex02_Fxn1.raw)
        • file_format (example: vendor-specific)
        • data_category (example: Raw Mass Spectra)
        • offset (required for pagination, example: 0)
        • limit (required for pagination, example: 10)
        Returns a list of files and a pagination record

        Fields:
        • total
        • files
        • pagination
        A test call can be issued with the following parameters:

        Parameters

        study_id
        string

        Study ID, example: 0fe15489-1381-4864-8b17-6159e14a65a8

        offset
        integer

        Offset of records, example: 0

        limit
        integer

        Limit of records, example: 10

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "getPaginatedFiles": {
              "total": 37809,
              "files": [
                {
                  "study_id": "0fe15489-1381-4864-8b17-6159e14a65a8",
                  "pdc_study_id": "PDC000431",
                  "study_submitter_id": "Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments",
                  "file_name": "BA20161122_BI_FM_Medullo_pY_Plex04_Fxn1.raw",
                  "file_id": "18ff9bcd-4e60-4949-9db0-b859c8d0b7bc",
                  "file_type": "Proprietary",
                  "file_format": "vendor-specific",
                  "data_category": "Raw Mass Spectra",
                  "md5sum": "058ab22afbf1fb18563f8e499ad3ad8d"
                }
              ]
            },
            "pagination": {
              "count": "10",
              "sort": "string",
              "from": "0",
              "page": "1",
              "total": "10",
              "pages": "1",
              "size": "10"
            }
          }
        }
        {} getPaginatedFiles
        datagetPaginatedFilesDef(optional)
        {} getPaginatedFilesDef
        getPaginatedFilesgetPaginatedFilesDesc(optional)
        paginationPagination(optional)
        {} getPaginatedFilesDesc
        totalnumber(optional)
        filesarray[filesForPaginatedRecords](optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
        {} filesForPaginatedRecords
        study_idstring(optional)
        pdc_study_idstring(optional)
        study_submitter_idstring(optional)
        file_namestring(optional)
        file_idstring(optional)
        file_typestring(optional)
        file_formatstring(optional)
        data_categorystring(optional)
        md5sumstring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000431)
        • file_name (example: 20151104-P50-20ug-s35.mzML.gz)
        • file_type (example: Proprietary)
        • data_category (example: Raw Mass Spectra)
        • file_format (example: vendor-specific)
        Returns a list of files per study. This API can also be used with multiple input parameters.
        It may take a long time to execute because of the huge volume of data.

        Fields:
        • study_id
        • pdc_study_id
        • study_submitter_id
        • study_name
        • file_id
        • file_name
        • file_submitter_id
        • file_type
        • md5sum
        • file_location
        • file_size
        • data_category
        • file_format
        • signedUrl {url}
        A test call can be issued with the following parameter:

        Parameters

        study_id
        string

        Study ID, example: 0fe15489-1381-4864-8b17-6159e14a65a8

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "filesPerStudy": [
              {
                "study_id": "0ea91a54-1798-11ea-9bfa-0a42f3c845fe",
                "pdc_study_id": "PDC000206",
                "study_submitter_id": "CPTAC GBM Discovery Study - CompRef Phosphoproteome",
                "study_name": "CPTAC GBM Discovery Study - CompRef Phosphoproteome",
                "file_id": "057a5b76-a582-4a3b-87d7-4897750d18c3",
                "file_name": "02CPTAC_CompRef_GBM_P_PNNL_20190306_B2S5_f10.mzML.gz",
                "file_submitter_id": "02CPTAC_CompRef_GBM_P_PNNL_20190306_B2S5_f10.mzML.gz",
                "file_type": "Open Standard",
                "md5sum": "058ab22afbf1fb18563f8e499ad3ad8d",
                "file_location": "studies/206/mzml/02CPTAC_CompRef_GBM_P_PNNL_20190306_B2S5_f10.mzML.gz",
                "file_size": "145180612",
                "data_category": "Processed Mass Spectra",
                "file_format": "mzML",
                "signedUrl": [
                  {
                    "url": "https://pdcdatastore.s3.amazonaws.com/studies/206/mzml/02CPTAC_CompRef_GBM_P_PNNL_20190306_B2S5_f10.mzML.gz?AWSAccessKeyId=AKIAQPWI5WIU7M4BLQXG&Expires=1602261172&Signature=W2wF3metuSJUtoZQQFkrfVX0dek%3D"
                  }
                ]
              }
            ]
          }
        }
        {} filesPerStudy
        datafilesPerStudyDef(optional)
        {} filesPerStudyDef
        filesPerStudyarray[filesPerStudyDesc](optional)
        {} filesPerStudyDesc
        study_idstring(optional)
        pdc_study_idstring(optional)
        study_submitter_idstring(optional)
        study_namestring(optional)
        file_idstring(optional)
        file_namestring(optional)
        file_submitter_idstring(optional)
        file_typestring(optional)
        md5sumstring(optional)
        file_locationstring(optional)
        file_sizestring(optional)
        data_categorystring(optional)
        file_formatstring(optional)
        signedUrlarray[signedUrlDesc](optional)
        {} signedUrlDesc
        urlstring(optional)
      • Show samples

        Returns spectral counts per study/aliquot/gene. This API can also be used with multiple input parameters.

        Fields:

        • total
        • spectralCounts
        • pagination

        Parameters

        study_id
        string

        Study ID, example: b93bb1e9-57b8-11e8-b07a-00a098d917f8

        plex_name
        string

        aliquot id, example: A2-A0D0-01A:BH-A0HK-01A:C8-A12T-01A:POOL

        gene_name
        string

        Name of gene, example: A2M

        offset
        integer

        Offset of records, example: 0

        limit
        integer

        Limit of records, example: 10

        acceptDUA
        boolean

        Accept DUA is no longer required

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "paginatedSpectralCountPerStudyAliquot": {
              "total": 1,
              "spectralCounts": [
                {
                  "study_id": "b93bb1e9-57b8-11e8-b07a-00a098d917f8",
                  "study_submitter_id": "TCGA BRCA Phosphoproteome S015-2",
                  "pdc_study_id": "PDC000174",
                  "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329",
                  "spectral_count": 94,
                  "distinct_peptide": 37,
                  "unshared_peptide": 36
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} paginatedSpectralCountPerStudyAliquot
        datapaginatedSpectralCountPerStudyAliquotDef(optional)
        {} paginatedSpectralCountPerStudyAliquotDef
        paginatedSpectralCountPerStudyAliquotpaginatedSpectralCountPerStudyAliquotDesc(optional)
        {} paginatedSpectralCountPerStudyAliquotDesc
        totalnumber(optional)
        spectralCountsarray[spectralCountsPaginatedAliquot](optional)
        paginationPagination(optional)
        {} spectralCountsPaginatedAliquot
        study_idstring(optional)
        study_submitter_idstring(optional)
        pdc_study_idstring(optional)
        plexstring(optional)
        spectral_countnumber(optional)
        distinct_peptidenumber(optional)
        unshared_peptidenumber(optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
      • Show samples

        Returns spectral counts per study/aliquot/gene. This API can also be used with multiple input parameters.

        Fields:

        • total
        • spectralCounts
        • pagination

        Parameters

        study_submitter_id
        string

        Submitter id of study, example: TCGA BRCA Phosphoproteome S015-2

        plex_name
        string

        aliquot id, example: A2-A0D0-01A:BH-A0HK-01A:C8-A12T-01A:POOL

        gene_name
        string

        Name of gene, example: A2M

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "paginatedSpectralCountPerStudyAliquot": {
              "total": 1,
              "spectralCounts": [
                {
                  "study_id": "b93bb1e9-57b8-11e8-b07a-00a098d917f8",
                  "study_submitter_id": "TCGA BRCA Phosphoproteome S015-2",
                  "pdc_study_id": "PDC000174",
                  "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329",
                  "spectral_count": 94,
                  "distinct_peptide": 37,
                  "unshared_peptide": 36
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} paginatedSpectralCountPerStudyAliquot
        datapaginatedSpectralCountPerStudyAliquotDef(optional)
        {} paginatedSpectralCountPerStudyAliquotDef
        paginatedSpectralCountPerStudyAliquotpaginatedSpectralCountPerStudyAliquotDesc(optional)
        {} paginatedSpectralCountPerStudyAliquotDesc
        totalnumber(optional)
        spectralCountsarray[spectralCountsPaginatedAliquot](optional)
        paginationPagination(optional)
        {} spectralCountsPaginatedAliquot
        study_idstring(optional)
        study_submitter_idstring(optional)
        pdc_study_idstring(optional)
        plexstring(optional)
        spectral_countnumber(optional)
        distinct_peptidenumber(optional)
        unshared_peptidenumber(optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
      • Show samples

        Returns spectral counts per study/aliquot/gene. This API can also be used with multiple input parameters.

        Fields:

        • total
        • spectralCounts
        • pagination

        Parameters

        pdc_study_id
        string

        Submitter id of study, example: PDC000174

        gene_name
        string

        Name of gene, example: A2M

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "paginatedSpectralCountPerStudyAliquot": {
              "total": 1,
              "spectralCounts": [
                {
                  "study_id": "b93bb1e9-57b8-11e8-b07a-00a098d917f8",
                  "study_submitter_id": "TCGA BRCA Phosphoproteome S015-2",
                  "pdc_study_id": "PDC000174",
                  "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329",
                  "spectral_count": 94,
                  "distinct_peptide": 37,
                  "unshared_peptide": 36
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} paginatedSpectralCountPerStudyAliquot
        datapaginatedSpectralCountPerStudyAliquotDef(optional)
        {} paginatedSpectralCountPerStudyAliquotDef
        paginatedSpectralCountPerStudyAliquotpaginatedSpectralCountPerStudyAliquotDesc(optional)
        {} paginatedSpectralCountPerStudyAliquotDesc
        totalnumber(optional)
        spectralCountsarray[spectralCountsPaginatedAliquot](optional)
        paginationPagination(optional)
        {} spectralCountsPaginatedAliquot
        study_idstring(optional)
        study_submitter_idstring(optional)
        pdc_study_idstring(optional)
        plexstring(optional)
        spectral_countnumber(optional)
        distinct_peptidenumber(optional)
        unshared_peptidenumber(optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
      • Show samples

        Input Parameter:

        • protein (example: M0R009)
        Returns spectral counts of available projects for gene to which the protein ID (Uniprot or Refseq) is mapped.

        Fields:
        • gene_name
        • NCBI_gene_id
        • authority
        • description
        • organism
        • chromosome
        • locus
        • proteins
        • assays
        • spectral_counts
        A test call can be issued with the following parameter (it may return slowly or even time out the first time due to the data volume. However, the result is cached and will be returned promptly if you try with the same parameter again):

        Parameters

        protein
        string

        Name of protein to return, example: M0R009

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "protein": {
              "gene_name": "A1BG",
              "NCBI_gene_id": 1,
              "authority": "HGNC:5",
              "description": "alpha-1-B glycoprotein",
              "organism": "Homo sapiens",
              "chromosome": "19",
              "locus": "19q13.43",
              "proteins": "M0R009;NP_570602.2;P04217;P04217-2",
              "assays": "non-CPTAC-1064",
              "spectral_counts": [
                {
                  "project_submitter_id": "CPTAC-TCGA",
                  "project_id": "48653303-5546-11e8-b664-00a098d917f8",
                  "plex": "06TCGA_A2-A0D0-01A_BH-A0HK-01A_C8-A12T-01A_Phosphoproteome_BI_20130329",
                  "spectral_count": "11",
                  "distinct_peptide": "5",
                  "unshared_peptide": "5",
                  "study_id": "bb67ec40-57b8-11e8-b07a-00a098d917f8",
                  "study_submitter_id": "S015-2",
                  "pdc_study_id": "PDC000174"
                }
              ]
            }
          }
        }
        {} Protein
        dataProteinDef(optional)
        {} ProteinDef
        proteinGene(optional)
        {} Gene
        gene_namestring(optional)
        NCBI_gene_idinteger(optional)
        authoritystring(optional)
        descriptionstring(optional)
        organismstring(optional)
        chromosomestring(optional)
        locusstring(optional)
        proteinsstring(optional)
        assaysstring(optional)
        spectral_countsarray[spectralCountsDesc](optional)
        {} spectralCountsDesc
        project_submitter_idstring(optional)
        project_idstring(optional)
        plexstring(optional)
        spectral_countnumber(optional)
        distinct_peptidenumber(optional)
        unshared_peptidenumber(optional)
        study_idstring(optional)
        study_submitter_idnumber(optional)
        pdc_study_idnumber(optional)
      • Show samples

        Returns quant data matrix for a PDC Study ID.
        Fields:

        • pdc_study_id: PDC Study ID, example: PDC000127
        • data_type: Data type, example: log2_ratio/unshared_log2_ratio
        • acceptDUA: Accept DUA , example: true/false
        This API also works with the following parameters:

        ?query= { quantDataMatrix(study_id: '{study_id}' data_type: '{data_type}' acceptDUA: {acceptDUA}) }

        Fields:
        • study_id: Study ID, example: dbe94609-1fb3-11e9-b7f8-0a80fada099c
        • data_type: Data type, example: log2_ratio/unshared_log2_ratio
        • acceptDUA: Accept DUA , example: true/false

        Please click here to know more on how to test this API.

        Test this endpoint

        Response Type

        Response Sample

        {
          "data": {
            "quantDataMatrix": [
              {
                "Gene/Aliquot": "string"
              }
            ]
          }
        }
        {} quantDataMatrix
        dataquantDataMatrixDef(optional)
        {} quantDataMatrixDef
        quantDataMatrixarray[quantDataMatrixDesc](optional)
        {} quantDataMatrixDesc
        Gene/Aliquotstring(optional)
      • Show samples

        Gets the following PDC metrics.

        Fields:

        • programs
        • projects
        • studies
        • cases
        • files
        • data_size_TB
        A test call can be issued by clicking the TRY button:

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "getPDCMetrics": [
              {
                "programs": 6,
                "projects": 13,
                "studies": 75,
                "cases": 2419,
                "files": 31172,
                "data_size_TB": 30
              }
            ]
          }
        }
        {} getPDCMetrics
        datagetPDCMetricsDef(optional)
        {} getPDCMetricsDef
        getPDCMetricsarray[getPDCMetricsDesc](optional)
        {} getPDCMetricsDesc
        programsinteger(optional)
        projectsinteger(optional)
        studiesinteger(optional)
        casesinteger(optional)
        filesinteger(optional)
        data_size_TBinteger(optional)
      • Show samples

        Gets the following PDC statistics.

        Fields:

        • program_id
        • program_submitter_id
        • name
        • project_count
        • study_count
        • data_file_count
        • data_size_TB
        A test call can be issued by clicking the TRY button:

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "dataStatsPerProgram": [
              {
                "program_id": "10251935-5540-11e8-b664-00a098d917f8",
                "program_submitter_id": "Georgetown Proteomics Research Program",
                "name": "Georgetown Proteomics Research Program",
                "project_count": 13,
                "study_count": 101,
                "data_file_count": 31172,
                "data_size_TB": 29
              }
            ]
          }
        }
        {} dataStatsPerProgram
        datadataStatsPerProgramDef(optional)
        {} dataStatsPerProgramDef
        dataStatsPerProgramarray[dataStatsPerProgramDesc](optional)
        {} dataStatsPerProgramDesc
        program_idstring(optional)
        program_submitter_idstring(optional)
        namestring(optional)
        project_countinteger(optional)
        study_countinteger(optional)
        data_file_countinteger(optional)
        data_size_TBinteger(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000127)
        Returns biospecimen details per study.

        Fields:
        • aliquot_id
        • sample_id
        • case_id
        • aliquot_submitter_id
        • sample_submitter_id
        • case_submitter_id
        • aliquot_status
        • case_status
        • sample_status
        • project_name
        • sample_type
        • disease_type
        • primary_site
        • pool
        • taxon
        • externalReferences { external_reference_id reference_resource_shortname reference_resource_name reference_entity_location }
        A test call can be issued with the following parameter:

        Parameters

        pdc_study_id
        string

        PDC Study ID, example: PDC000127

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "biospecimenPerStudy": [
              {
                "aliquot_id": "bd34fbb3-2053-11e9-b7f8-0a80fada099c",
                "sample_id": "b72322c6-204c-11e9-b7f8-0a80fada099c",
                "case_id": "dae8930e-1fb8-11e9-b7f8-0a80fada099c",
                "aliquot_submitter_id": "CPT0026410003",
                "sample_submitter_id": "C3L-00791-01",
                "case_submitter_id": "C3L-00791",
                "aliquot_status": "Qualified",
                "case_status": "Qualified",
                "sample_status": "Qualified",
                "project_name": "CPTAC3 Discovery",
                "sample_type": "Primary Tumor",
                "disease_type": "Clear Cell Renal Cell Carcinoma",
                "primary_site": "Kidney",
                "pool": "No",
                "taxon": "Homo sapiens",
                "externalReferences": [
                  {
                    "external_reference_id": "ad9a7ce1-9f9e-4092-8eae-493297289022",
                    "reference_resource_shortname": "GDC",
                    "reference_resource_name": "Genomic Data Commons",
                    "reference_entity_location": "https://portal.gdc.cancer.gov/cases/ad9a7ce1-9f9e-4092-8eae-493297289022"
                  }
                ]
              }
            ]
          }
        }
        {} biospecimenPerStudy
        databiospecimenPerStudyDef(optional)
        {} biospecimenPerStudyDef
        biospecimenPerStudyarray[biospecimenPerStudyDesc](optional)
        {} biospecimenPerStudyDesc
        aliquot_idstring(optional)
        sample_idstring(optional)
        case_idstring(optional)
        aliquot_submitter_idstring(optional)
        sample_submitter_idstring(optional)
        case_submitter_idstring(optional)
        aliquot_statusstring(optional)
        case_statusstring(optional)
        sample_statusstring(optional)
        project_namestring(optional)
        sample_typestring(optional)
        disease_typestring(optional)
        primary_sitestring(optional)
        poolstring(optional)
        taxonstring(optional)
        externalReferencesarray[ExternalReferencesBipspecimen](optional)
        {} ExternalReferencesBipspecimen
        external_reference_idstring(optional)
        reference_resource_shortnamestring(optional)
        reference_resource_namestring(optional)
        reference_entity_locationstring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000127)
        Gets protocols per study.

        Fields:
        • protocol_id
        • protocol_submitter_id
        • study_id
        • pdc_study_id
        • study_submitter_id
        • program_id
        • program_submitter_id
        • protocol_name
        • protocol_date
        • document_name
        • quantitation_strategy
        • experiment_type
        • label_free_quantitation
        • labeled_quantitation
        • isobaric_labeling_reagent
        • reporter_ion_ms_level
        • starting_amount
        • starting_amount_uom
        • digestion_reagent
        • alkylation_reagent
        • enrichment_strategy
        • enrichment
        • chromatography_dimensions_count
        • one_d_chromatography_type
        • two_d_chromatography_type
        • fractions_analyzed_count
        • column_type
        • amount_on_column
        • amount_on_column_uom
        • column_length
        • column_length_uom
        • column_inner_diameter
        • column_inner_diameter_uom
        • particle_size
        • particle_size_uom
        • particle_type
        • gradient_length
        • gradient_length_uom
        • instrument_make
        • instrument_model
        • dissociation_type
        • ms1_resolution
        • ms2_resolution
        • dda_topn
        • normalized_collision_energy
        • acquistion_type
        • dia_multiplexing
        • dia_ims
        • analytical_technique
        • chromatography_instrument_make
        • chromatography_instrument_model
        • polarity
        • reconstitution_solvent
        • reconstitution_volume
        • reconstitution_volume_uom
        • internal_standards
        • extraction_method
        • ionization_mode
        A test call can be issued with the following parameter:

        Parameters

        study_submitter_id
        string

        Submitter id of study, example: TCGA BRCA Phosphoproteome S015-2

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "protocolPerStudy": [
              {
                "protocol_id": "1c06aff5-3b26-11e9-9a07-0a80fada099c",
                "protocol_submitter_id": "P-S015-2",
                "study_id": "b93bb1e9-57b8-11e8-b07a-00a098d917f8",
                "pdc_study_id": "PDC000174",
                "study_submitter_id": "TCGA BRCA Phosphoproteome S015-2",
                "program_id": "10251935-5540-11e8-b664-00a098d917f8",
                "program_submitter_id": "CPTAC",
                "protocol_name": "TCGA_Breast_Cancer_Phosphoproteome",
                "protocol_date": "2013-02-02",
                "document_name": " ",
                "quantitation_strategy": "Isobaric label quantitation",
                "experiment_type": "iTRAQ4",
                "label_free_quantitation": " ",
                "labeled_quantitation": "iTRAQ quantitation",
                "isobaric_labeling_reagent": "iTRAQ",
                "reporter_ion_ms_level": "2",
                "starting_amount": "4.00",
                "starting_amount_uom": "mg",
                "digestion_reagent": "Lys-C/Trypsin",
                "alkylation_reagent": "Iodoacetamide",
                "enrichment_strategy": "Phosphoproteome",
                "enrichment": "Phosphopeptide enrichment with immobilized metal affinity chromatography (NiNTA beads stripped with EDTA and loaded with FeCl3; Qiagen)",
                "chromatography_dimensions_count": "2",
                "one_d_chromatography_type": "bRPLC (pH 10)",
                "two_d_chromatography_type": "RPLC",
                "fractions_analyzed_count": "13",
                "column_type": "New Objective; PicoFrit SELF/P",
                "amount_on_column": " ",
                "amount_on_column_uom": " ",
                "column_length": "20",
                "column_length_uom": "cm",
                "column_inner_diameter": "75",
                "column_inner_diameter_uom": "µm",
                "particle_size": "1.9",
                "particle_size_uom": "µm",
                "particle_type": "Dr Maisch GmbH; ReproSil-Pur 120 C18-AQ; 1.9 um",
                "gradient_length": "110",
                "gradient_length_uom": "min",
                "instrument_make": "Thermo Scientific",
                "instrument_model": "Q Exactive",
                "dissociation_type": "HCD",
                "ms1_resolution": "70000",
                "ms2_resolution": "17500",
                "dda_topn": "Top12",
                "normalized_collision_energy": "28%",
                "acquistion_type": "DDA",
                "dia_multiplexing": "N/A",
                "dia_ims": "N/A",
                "analytical_technique": "N/A",
                "chromatography_instrument_make": "N/A",
                "chromatography_instrument_model": "N/A",
                "polarity": "N/A",
                "reconstitution_solvent": "N/A",
                "reconstitution_volume": "N/A",
                "reconstitution_volume_uom": "N/A",
                "internal_standards": "N/A",
                "extraction_method": "N/A",
                "ionization_mode": "N/A"
              }
            ]
          }
        }
        {} protocolPerStudy
        dataprotocolPerStudyDef(optional)
        {} protocolPerStudyDef
        protocolPerStudyarray[protocolPerStudyDesc](optional)
        {} protocolPerStudyDesc
        protocol_idstring(optional)
        protocol_submitter_idstring(optional)
        study_idstring(optional)
        pdc_study_idstring(optional)
        study_submitter_idstring(optional)
        program_idstring(optional)
        program_submitter_idstring(optional)
        protocol_namestring(optional)
        protocol_datestring(optional)
        document_namestring(optional)
        quantitation_strategystring(optional)
        experiment_typestring(optional)
        label_free_quantitationstring(optional)
        labeled_quantitationstring(optional)
        isobaric_labeling_reagentstring(optional)
        reporter_ion_ms_levelstring(optional)
        starting_amountstring(optional)
        starting_amount_uomstring(optional)
        digestion_reagentstring(optional)
        alkylation_reagentstring(optional)
        enrichment_strategystring(optional)
        enrichmentstring(optional)
        chromatography_dimensions_countstring(optional)
        one_d_chromatography_typestring(optional)
        two_d_chromatography_typestring(optional)
        fractions_analyzed_countstring(optional)
        column_typestring(optional)
        amount_on_columnstring(optional)
        amount_on_column_uomstring(optional)
        column_lengthstring(optional)
        column_length_uomstring(optional)
        column_inner_diameterstring(optional)
        column_inner_diameter_uomstring(optional)
        particle_sizestring(optional)
        particle_size_uomstring(optional)
        particle_typestring(optional)
        gradient_lengthstring(optional)
        gradient_length_uomstring(optional)
        instrument_makestring(optional)
        instrument_modelstring(optional)
        dissociation_typestring(optional)
        ms1_resolutionstring(optional)
        ms2_resolutionstring(optional)
        dda_topnstring(optional)
        normalized_collision_energystring(optional)
        acquistion_typestring(optional)
        dia_multiplexingstring(optional)
        dia_imsstring(optional)
        analytical_techniquestring(optional)
        chromatography_instrument_makestring(optional)
        chromatography_instrument_modelstring(optional)
        polaritystring(optional)
        reconstitution_solventstring(optional)
        reconstitution_volumestring(optional)
        reconstitution_volume_uomstring(optional)
        internal_standardsstring(optional)
        extraction_methodstring(optional)
        ionization_modestring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • entity_type (example: study or case)
        • entity_id (must be the id of an object of the entity_type entered. example: dbe94609-1fb3-11e9-b7f8-0a80fada099c)
        • reference_type (example: internal/external)
        Returns details of a study

        Fields:
        • pdcEntityReference
        A test call can be issued with the following parameters:

        Parameters

        entity_type
        string

        Entity type, example: study or case

        entity_id
        string

        Entity ID, example: 85df2ad5-0c83-4674-8013-0d6f360b9831 for study or bc2e2a27-9d23-4749-a2b4-ce6bbcad85b7 for case

        reference_type
        string

        Reference type, example: external

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "pdcEntityReference": [
              {
                "reference_id": "25b2ff66-88bc-11ea-bc9a-0a16d369a41f",
                "entity_type": "study",
                "entity_id": "dbe94609-1fb3-11e9-b7f8-0a80fada099c",
                "reference_type": "external",
                "reference_entity_type": "study",
                "reference_entity_alias": "S044",
                "reference_resource_name": "Clinical Proteomic Tumor Analysis Consortium",
                "reference_resource_shortname": "CPTAC",
                "reference_entity_location": "https://cptac-data-portal.georgetown.edu/cptac/s/S044\r"
              }
            ]
          }
        }
        {} pdcEntityReference
        datapdcEntityReferenceDef(optional)
        {} pdcEntityReferenceDef
        pdcEntityReferencearray[pdcEntityReferenceDetails](optional)
        {} pdcEntityReferenceDetails
        reference_idstring(optional)
        entity_typestring(optional)
        entity_idstring(optional)
        reference_typestring(optional)
        reference_entity_typestring(optional)
        reference_entity_aliasstring(optional)
        reference_resource_namestring(optional)
        reference_resource_shortnamestring(optional)
        reference_entity_locationstring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • entity_type (example: diagnosis)
        • entity_id (must be the id of an object of the entity_type entered. example: d0913803-ff5e-11e9-9a07-0a80fada099c)
        • reference_type (example: internal)
        Returns details of an entity reference

        Fields:
        • reference
        A test call can be issued with the following parameters:

        Parameters

        entity_type
        string

        Entity type, example: diagnosis

        entity_id
        string

        Entity ID: example: diagnosis ID:d0913803-ff5e-11e9-9a07-0a80fada099c

        reference_type
        string

        Reference type, example: internal

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "reference": [
              {
                "reference_id": "25b2ff66-88bc-11ea-bc9a-0a16d369a41f",
                "entity_type": "diagnosis",
                "entity_id": "d0913803-ff5e-11e9-9a07-0a80fada099c",
                "reference_type": "internal",
                "reference_entity_type": "sample",
                "reference_entity_alias": "7316-496",
                "reference_resource_name": "Proteomic Data Commons",
                "reference_resource_shortname": "PDC",
                "reference_entity_location": "string"
              }
            ]
          }
        }
        {} reference
        datareferenceDef(optional)
        {} referenceDef
        referencearray[referenceDetails](optional)
        {} referenceDetails
        reference_idstring(optional)
        entity_typestring(optional)
        entity_idstring(optional)
        reference_typestring(optional)
        reference_entity_typestring(optional)
        reference_entity_aliasstring(optional)
        reference_resource_namestring(optional)
        reference_resource_shortnamestring(optional)
        reference_entity_locationstring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • tissue_or_organ_of_origin (example: Breast)
        • project_submitter_id (example: CPTAC-2)
        • project_id (example: d78374f9-5fd5-4776-aa41-b1fe7ef338ab)
        Returns a list of Tissue Sites.

        Fields:
        • tissue_or_organ_of_origin:Text term that describes the anatomic site of the tumor or disease. caDSR: 3427536, example: Breast
        • project_id
        • project_submitter_id
        • cases_count
        A test call can be issued by clicking the TRY button:

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "tissueSitesAvailable": [
              {
                "tissue_or_organ_of_origin": "Breast",
                "project_id": "d78374f9-5fd5-4776-aa41-b1fe7ef338ab",
                "project_submitter_id": "CPTAC-2",
                "cases_count": 119
              }
            ]
          }
        }
        {} tissueSitesAvailable
        datatissueSitesAvailableDef(optional)
        {} tissueSitesAvailableDef
        tissueSitesAvailablearray[tissueSitesAvailableDesc](optional)
        {} tissueSitesAvailableDesc
        tissue_or_organ_of_originstring(optional)
        project_idstring(optional)
        project_submitter_idstring(optional)
        cases_countnumber(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • disease_type (example: Colon Adenocarcinoma)
        • year (example: 2015)
        • pubmed_id (example: 26110064)
        • offset (required for pagination, example: 0)
        • limit (required for pagination, example: 10)
        Returns a list of publications.

        Fields:
        • publication_id
        • pubmed_id
        • doi
        • author
        • title
        • journal
        • journal_url
        • year
        • abstract
        • citation
        • studies
        • disease_types
        A test call can be issued by clicking the TRY button:

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "getPaginatedPublications": {
              "total": "44",
              "uiPublication": [
                {
                  "publication_id": "18a56fbd-10d5-11e9-afb9-0a9c39d33490",
                  "pubmed_id": "25730263",
                  "doi": "10.1038/nm.3807",
                  "author": "Guo, T.; Kouvonen, P.; Koh, C. C.; Gillet, L. C.; Wolski, W. E.; Röst, H. L....",
                  "title": "Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps",
                  "journal": "Nat Med",
                  "journal_url": "https://www.nature.com/articles/nm.3807",
                  "year": "2015",
                  "abstract": "Clinical specimens are each inherently unique, limited and nonrenewable....",
                  "citation": "uo, T., Kouvonen, P., Koh, C.C., et al. (2015)....",
                  "studies": [
                    {
                      "pdc_study_id": "PDC000152",
                      "submitter_id_name": "PCT SWATH Kidney"
                    }
                  ],
                  "disease_types": " [Clear Cell Renal Cell Carcinoma, Papillary Renal Cell Carcinoma, Chromophobe Renal Cell Carcinoma]"
                }
              ],
              "pagination": {
                "count": "10",
                "sort": "string",
                "from": "0",
                "page": "1",
                "total": "10",
                "pages": "1",
                "size": "10"
              }
            }
          }
        }
        {} getPaginatedPublications
        datagetPaginatedPublicationsDef(optional)
        {} getPaginatedPublicationsDef
        getPaginatedPublicationsgetPaginatedPublicationsDesc(optional)
        {} getPaginatedPublicationsDesc
        totalnumber(optional)
        uiPublicationarray[uiPublication](optional)
        paginationPagination(optional)
        {} uiPublication
        publication_idstring(optional)
        pubmed_idstring(optional)
        doinumber(optional)
        authorstring(optional)
        titlestring(optional)
        journalstring(optional)
        journal_urlstring(optional)
        yearstring(optional)
        abstractstring(optional)
        citationstring(optional)
        studiesarray[pubStudies](optional)
        disease_typesstring(optional)
        {} Pagination
        countinteger
        sortstring(optional)
        frominteger
        pageinteger
        totalinteger
        pagesinteger
        sizeinteger
        {} pubStudies
        pdc_study_idstring(optional)
        submitter_id_namestring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: 0fe15489-1381-4864-8b17-6159e14a65a8)
        • study_submitter_id (example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments)
        • pdc_study_id (example: PDC000431)
        Fields:
        • experiment_type
        • analytical_fraction
        • instrument
        • study_run_metadata
        • files
        A test call can be issued with the following parameter:

        Parameters

        study_submitter_id
        string

        Study submitter ID, example: Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "experimentalMetadata": [
              {
                "experiment_type": "iTRAQ4",
                "analytical_fraction": "Phosphoproteome",
                "instrument": "Q Exactive",
                "study_run_metadata": [
                  {
                    "study_run_metadata_id": "d9b03458-56ca-11e8-b664-00a098d917f8",
                    "study_run_metadata_submitter_id": "S015-2-27",
                    "fraction": "1-12, A",
                    "aliquot_run_metadata": [
                      {
                        "aliquot_id": "141959ca-6424-11e8-bcf1-0a2705229b82",
                        "aliquot_submitter_id": "TCGA-AO-A12B-01A-41-A21V-30",
                        "aliquot_run_metadata_id": "2384aae1-5732-11e8-b664-00a098d917f8",
                        "label": "itraq_116",
                        "experiment_number": "13",
                        "fraction": "24-Jan",
                        "replicate_number": "1",
                        "date": "2013-02-28",
                        "alias": "B1S6",
                        "analyte": "Proteome"
                      }
                    ],
                    "files": [
                      {
                        "file_type": "Proprietary",
                        "data_category": "Raw Mass Spectra",
                        "file_location": "raw-files/10/30/TCGA_A2-A0YG_E2-A150_BH-A18N_117C_P_BI_20130920_H-PM_f07.raw"
                      }
                    ]
                  }
                ]
              }
            ]
          }
        }
        {} experimentalMetadata
        dataexperimentalMetadataDef(optional)
        {} experimentalMetadataDef
        experimentalMetadataarray[experimentalMetadataDesc](optional)
        {} experimentalMetadataDesc
        experiment_typestring(optional)
        analytical_fractionstring(optional)
        instrumentstring(optional)
        study_run_metadataarray[Study_run_metadata](optional)
        {} Study_run_metadata
        study_run_metadata_idstring(optional)
        study_run_metadata_submitter_idstring(optional)
        fractionstring(optional)
        aliquot_run_metadataarray[Aliquot_run_metadata](optional)
        filesarray[fileInformation](optional)
        {} Aliquot_run_metadata
        aliquot_idstring(optional)
        aliquot_submitter_idstring(optional)
        aliquot_run_metadata_idstring(optional)
        labelstring(optional)
        experiment_numberstring(optional)
        fractionstring(optional)
        replicate_numberstring(optional)
        datestring(optional)
        aliasstring(optional)
        analytestring(optional)
        {} fileInformation
        file_typestring(optional)
        data_categorystring(optional)
        file_locationstring(optional)
      • Show samples

        Input Parameters (multiple parameters can be passed in one call):

        • study_id (example: dbe94609-1fb3-11e9-b7f8-0a80fada099c)
        • study_submitter_id (example: CPTAC CCRCC Discovery Study - Proteome S044-1)
        • pdc_study_id (example: PDC000127)
        Gets Study details.

        Fields:
        • study_id
        • pdc_study_id
        • study_submitter_id
        • program_id
        • project_id
        • study_name
        • study_description
        • program_name
        • project_name
        • disease_type
        • primary_site
        • analytical_fraction
        • experiment_type
        • cases_count
        • aliquots_count
        • filesCount
        A test call can be issued with the following parameter:

        Parameters

        pdc_study_id
        string

        PDC Study ID, example: PDC000127

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "study": [
              {
                "study_id": "dbe94609-1fb3-11e9-b7f8-0a80fada099c",
                "pdc_study_id": "PDC000127",
                "study_submitter_id": "S044-1",
                "program_id": "10251935-5540-11e8-b664-00a098d917f8",
                "project_id": "267d6671-0e78-11e9-a064-0a9c39d33490",
                "study_name": "CPTAC CCRCC Discovery Study - Proteome",
                "study_description": "Kidney cancer is among the 10 most common cancers...",
                "program_name": "Clinical Proteomic Tumor Analysis Consortium",
                "project_name": "CPTAC3 Discovery",
                "disease_type": "Clear Cell Renal Cell Carcinoma;Other",
                "primary_site": "Kidney;N/A",
                "analytical_fraction": "Proteome",
                "experiment_type": "TMT10",
                "cases_count": 126,
                "aliquots_count": 218,
                "filesCount": [
                  {
                    "data_category": "Other Metadata",
                    "file_type": "Document",
                    "files_count": 7
                  }
                ]
              }
            ]
          }
        }
        {} studyDetailsPerStudyID
        datastudyDetailsPerStudyIDDef(optional)
        {} studyDetailsPerStudyIDDef
        studyarray[studyDetailsPerStudyIDDesc](optional)
        {} studyDetailsPerStudyIDDesc
        study_idstring(optional)
        pdc_study_idstring(optional)
        study_submitter_idstring(optional)
        program_idstring(optional)
        project_idstring(optional)
        study_namestring(optional)
        study_descriptionstring(optional)
        program_namestring(optional)
        project_namestring(optional)
        disease_typestring(optional)
        primary_sitestring(optional)
        analytical_fractionstring(optional)
        experiment_typestring(optional)
        cases_countnumber(optional)
        aliquots_countnumber(optional)
        filesCountarray[fileDetailsPerStudyIDDesc](optional)
        {} fileDetailsPerStudyIDDesc
        data_categorystring(optional)
        file_typenumber(optional)
        files_countnumber(optional)
      • Show samples

        Gets Studies with version information.

        Fields:

        • pdc_study_id
        • versions

        Parameters

        acceptDUA
        boolean

        Accept DUA is no longer required

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "studyCatalog": [
              {
                "pdc_study_id": "PDC000121",
                "versions": [
                  {
                    "study_id": "b91a0e5f-f3a0-11ea-b1fd-0aad30af8a83",
                    "study_submitter_id": "Prospective Breast BI Phosphoproteome v2",
                    "submitter_id_name": "Prospective Breast BI Phosphoproteome",
                    "study_shortname": "Prospective BRCA Phosphoproteome S039-2",
                    "study_version": "2",
                    "is_latest_version": "yes/no"
                  }
                ]
              }
            ]
          }
        }
        {} studyCatalog
        datastudyCatalogDef(optional)
        {} studyCatalogDef
        studyCatalogarray[studyCatalogDesc](optional)
        {} studyCatalogDesc
        pdc_study_idstring(optional)
        versionsarray[versionDesc](optional)
        {} versionDesc
        study_idstring(optional)
        study_submitter_idstring(optional)
        submitter_id_namestring(optional)
        study_shortnamestring(optional)
        study_versionstring(optional)
        is_latest_versionstring(optional)
      • Show samples

        Gets Studies with version information for a specific pdc_study_id.

        Fields:

        • pdc_study_id
        • versions

        Parameters

        pdc_study_id
        string

        PDC Study ID, example: PDC000121

        acceptDUA
        boolean

        Accept DUA is no longer required

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "studyCatalog": [
              {
                "pdc_study_id": "PDC000121",
                "versions": [
                  {
                    "study_id": "b91a0e5f-f3a0-11ea-b1fd-0aad30af8a83",
                    "study_submitter_id": "Prospective Breast BI Phosphoproteome v2",
                    "submitter_id_name": "Prospective Breast BI Phosphoproteome",
                    "study_shortname": "Prospective BRCA Phosphoproteome S039-2",
                    "study_version": "2",
                    "is_latest_version": "yes/no"
                  }
                ]
              }
            ]
          }
        }
        {} studyCatalog
        datastudyCatalogDef(optional)
        {} studyCatalogDef
        studyCatalogarray[studyCatalogDesc](optional)
        {} studyCatalogDesc
        pdc_study_idstring(optional)
        versionsarray[versionDesc](optional)
        {} versionDesc
        study_idstring(optional)
        study_submitter_idstring(optional)
        submitter_id_namestring(optional)
        study_shortnamestring(optional)
        study_versionstring(optional)
        is_latest_versionstring(optional)
      • Show samples

        Returns a list of workflow metadata. This API can also be used with multiple input parameters.

        Fields:

        • workflow_metadata_id
        • study_id
        • protocol_id
        • workflow_metadata_submitter_id
        • pdc_study_id
        • study_submitter_id
        • protocol_submitter_id
        • cptac_study_id
        • submitter_id_name
        • study_submitter_name
        • analytical_fraction
        • experiment_type
        • instrument
        • refseq_database_version
        • uniport_database_version
        • hgnc_version
        • raw_data_processing
        • raw_data_conversion
        • sequence_database_search
        • search_database_parameters
        • phosphosite_localization
        • ms1_data_analysis
        • psm_report_generation
        • cptac_dcc_mzidentml
        • mzidentml_refseq
        • mzidentml_uniprot
        • gene_to_prot
        • cptac_galaxy_workflows
        • cptac_galaxy_tools
        • cdap_reports
        • cptac_dcc_tools

        Parameters

        acceptDUA
        boolean

        Accept DUA is no longer required

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "workflowMetadata": [
              {
                "workflow_metadata_id": "b67c62e9-5766-11e8-b664-00a098d917f8",
                "study_id": "b9f2ccc5-57b8-11e8-b07a-00a098d917f8",
                "protocol_id": "05a47af4-571e-11e8-b664-00a098d917f8",
                "workflow_metadata_submitter_id": "TCGA_Breast_Cancer_Proteome",
                "pdc_study_id": "PDC000173",
                "study_submitter_id": "S015-1",
                "protocol_submitter_id": "P-S015-1",
                "cptac_study_id": "S015",
                "submitter_id_name": "MSGF+ iTRAQ 4-plex (Thermo Q-Exactive HCD)",
                "study_submitter_name": "TCGA_Breast_Cancer_Proteome",
                "analytical_fraction": "Proteome",
                "experiment_type": "iTRAQ4",
                "instrument": "Thermo Q Exactive",
                "refseq_database_version": "RefSeq human build 37",
                "uniport_database_version": "N/A",
                "hgnc_version": "string",
                "raw_data_processing": "ReAdw4Mascot2.exe version 1.2 ConvVer 20130604a",
                "raw_data_conversion": "msconvert 3.0.3827",
                "sequence_database_search": "MSGF+ v9733",
                "search_database_parameters": "java –Xmx3500M –jar MSGFPlus.jar -d <file>.fasta -t 20ppm -e 1 -m (3 for QExactive, 1 for Orbitrap) -inst (1 for QExactive, 1 for Orbitrap) -ntt 1 -thread 2 -tda 1 -ti 0,1 -n 1 -maxLength 50 -mod <file>.txt",
                "phosphosite_localization": "string",
                "ms1_data_analysis": "ProMS",
                "psm_report_generation": "single_file_report.exe",
                "cptac_dcc_mzidentml": "1.2.2",
                "mzidentml_refseq": "r82",
                "mzidentml_uniprot": "2017_06",
                "gene_to_prot": "2017-07-20",
                "cptac_galaxy_workflows": "N/A",
                "cptac_galaxy_tools": "N/A",
                "cdap_reports": "N/A",
                "cptac_dcc_tools": "N/A"
              }
            ]
          }
        }
        {} workflowMetadata
        dataworkflowMetadataDef(optional)
        {} workflowMetadataDef
        workflowMetadataarray[workflowMetadataDesc](optional)
        {} workflowMetadataDesc
        workflow_metadata_idstring(optional)
        study_idstring(optional)
        protocol_idstring(optional)
        workflow_metadata_submitter_idstring(optional)
        pdc_study_idstring(optional)
        study_submitter_idstring(optional)
        protocol_submitter_idstring(optional)
        cptac_study_idstring(optional)
        submitter_id_namestring(optional)
        study_submitter_namestring(optional)
        analytical_fractionstring(optional)
        experiment_typestring(optional)
        instrumentstring(optional)
        refseq_database_versionstring(optional)
        uniport_database_versionstring(optional)
        hgnc_versionstring(optional)
        raw_data_processingstring(optional)
        raw_data_conversionstring(optional)
        sequence_database_searchstring(optional)
        search_database_parametersstring(optional)
        phosphosite_localizationstring(optional)
        ms1_data_analysisstring(optional)
        psm_report_generationstring(optional)
        cptac_dcc_mzidentmlstring(optional)
        mzidentml_refseqstring(optional)
        mzidentml_uniprotstring(optional)
        gene_to_protstring(optional)
        cptac_galaxy_workflowsstring(optional)
        cptac_galaxy_toolsstring(optional)
        cdap_reportsstring(optional)
        cptac_dcc_toolsstring(optional)
      • Show samples

        Returns a list of workflow metadata. This API can also be used with multiple input parameters.

        Fields:

        • workflow_metadata_id
        • study_id
        • protocol_id
        • workflow_metadata_submitter_id
        • pdc_study_id
        • study_submitter_id
        • protocol_submitter_id
        • cptac_study_id
        • submitter_id_name
        • study_submitter_name
        • analytical_fraction
        • experiment_type
        • instrument
        • refseq_database_version
        • uniport_database_version
        • hgnc_version
        • raw_data_processing
        • raw_data_conversion
        • sequence_database_search
        • search_database_parameters
        • phosphosite_localization
        • ms1_data_analysis
        • psm_report_generation
        • cptac_dcc_mzidentml
        • mzidentml_refseq
        • mzidentml_uniprot
        • gene_to_prot
        • cptac_galaxy_workflows
        • cptac_galaxy_tools
        • cdap_reports
        • cptac_dcc_tools

        Parameters

        study_id
        string

        Study ID, example: b9f2ccc5-57b8-11e8-b07a-00a098d917f8

        acceptDUA
        boolean

        Accept DUA is no longer required

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "workflowMetadata": [
              {
                "workflow_metadata_id": "b67c62e9-5766-11e8-b664-00a098d917f8",
                "study_id": "b9f2ccc5-57b8-11e8-b07a-00a098d917f8",
                "protocol_id": "05a47af4-571e-11e8-b664-00a098d917f8",
                "workflow_metadata_submitter_id": "TCGA_Breast_Cancer_Proteome",
                "pdc_study_id": "PDC000173",
                "study_submitter_id": "S015-1",
                "protocol_submitter_id": "P-S015-1",
                "cptac_study_id": "S015",
                "submitter_id_name": "MSGF+ iTRAQ 4-plex (Thermo Q-Exactive HCD)",
                "study_submitter_name": "TCGA_Breast_Cancer_Proteome",
                "analytical_fraction": "Proteome",
                "experiment_type": "iTRAQ4",
                "instrument": "Thermo Q Exactive",
                "refseq_database_version": "RefSeq human build 37",
                "uniport_database_version": "N/A",
                "hgnc_version": "string",
                "raw_data_processing": "ReAdw4Mascot2.exe version 1.2 ConvVer 20130604a",
                "raw_data_conversion": "msconvert 3.0.3827",
                "sequence_database_search": "MSGF+ v9733",
                "search_database_parameters": "java –Xmx3500M –jar MSGFPlus.jar -d <file>.fasta -t 20ppm -e 1 -m (3 for QExactive, 1 for Orbitrap) -inst (1 for QExactive, 1 for Orbitrap) -ntt 1 -thread 2 -tda 1 -ti 0,1 -n 1 -maxLength 50 -mod <file>.txt",
                "phosphosite_localization": "string",
                "ms1_data_analysis": "ProMS",
                "psm_report_generation": "single_file_report.exe",
                "cptac_dcc_mzidentml": "1.2.2",
                "mzidentml_refseq": "r82",
                "mzidentml_uniprot": "2017_06",
                "gene_to_prot": "2017-07-20",
                "cptac_galaxy_workflows": "N/A",
                "cptac_galaxy_tools": "N/A",
                "cdap_reports": "N/A",
                "cptac_dcc_tools": "N/A"
              }
            ]
          }
        }
        {} workflowMetadata
        dataworkflowMetadataDef(optional)
        {} workflowMetadataDef
        workflowMetadataarray[workflowMetadataDesc](optional)
        {} workflowMetadataDesc
        workflow_metadata_idstring(optional)
        study_idstring(optional)
        protocol_idstring(optional)
        workflow_metadata_submitter_idstring(optional)
        pdc_study_idstring(optional)
        study_submitter_idstring(optional)
        protocol_submitter_idstring(optional)
        cptac_study_idstring(optional)
        submitter_id_namestring(optional)
        study_submitter_namestring(optional)
        analytical_fractionstring(optional)
        experiment_typestring(optional)
        instrumentstring(optional)
        refseq_database_versionstring(optional)
        uniport_database_versionstring(optional)
        hgnc_versionstring(optional)
        raw_data_processingstring(optional)
        raw_data_conversionstring(optional)
        sequence_database_searchstring(optional)
        search_database_parametersstring(optional)
        phosphosite_localizationstring(optional)
        ms1_data_analysisstring(optional)
        psm_report_generationstring(optional)
        cptac_dcc_mzidentmlstring(optional)
        mzidentml_refseqstring(optional)
        mzidentml_uniprotstring(optional)
        gene_to_protstring(optional)
        cptac_galaxy_workflowsstring(optional)
        cptac_galaxy_toolsstring(optional)
        cdap_reportsstring(optional)
        cptac_dcc_toolsstring(optional)
      • Show samples

        Returns a list of workflow metadata. This API can also be used with multiple input parameters.

        Fields:

        • workflow_metadata_id
        • study_id
        • protocol_id
        • workflow_metadata_submitter_id
        • pdc_study_id
        • study_submitter_id
        • protocol_submitter_id
        • cptac_study_id
        • submitter_id_name
        • study_submitter_name
        • analytical_fraction
        • experiment_type
        • instrument
        • refseq_database_version
        • uniport_database_version
        • hgnc_version
        • raw_data_processing
        • raw_data_conversion
        • sequence_database_search
        • search_database_parameters
        • phosphosite_localization
        • ms1_data_analysis
        • psm_report_generation
        • cptac_dcc_mzidentml
        • mzidentml_refseq
        • mzidentml_uniprot
        • gene_to_prot
        • cptac_galaxy_workflows
        • cptac_galaxy_tools
        • cdap_reports
        • cptac_dcc_tools

        Parameters

        pdc_study_id
        string

        PDC Study ID, example: PDC000174

        acceptDUA
        boolean

        Accept DUA is no longer required

        Test this endpoint

        Response Type

        Response Messages

        401 Unauthorized

        Response Sample

        {
          "data": {
            "workflowMetadata": [
              {
                "workflow_metadata_id": "b67c62e9-5766-11e8-b664-00a098d917f8",
                "study_id": "b9f2ccc5-57b8-11e8-b07a-00a098d917f8",
                "protocol_id": "05a47af4-571e-11e8-b664-00a098d917f8",
                "workflow_metadata_submitter_id": "TCGA_Breast_Cancer_Proteome",
                "pdc_study_id": "PDC000173",
                "study_submitter_id": "S015-1",
                "protocol_submitter_id": "P-S015-1",
                "cptac_study_id": "S015",
                "submitter_id_name": "MSGF+ iTRAQ 4-plex (Thermo Q-Exactive HCD)",
                "study_submitter_name": "TCGA_Breast_Cancer_Proteome",
                "analytical_fraction": "Proteome",
                "experiment_type": "iTRAQ4",
                "instrument": "Thermo Q Exactive",
                "refseq_database_version": "RefSeq human build 37",
                "uniport_database_version": "N/A",
                "hgnc_version": "string",
                "raw_data_processing": "ReAdw4Mascot2.exe version 1.2 ConvVer 20130604a",
                "raw_data_conversion": "msconvert 3.0.3827",
                "sequence_database_search": "MSGF+ v9733",
                "search_database_parameters": "java –Xmx3500M –jar MSGFPlus.jar -d <file>.fasta -t 20ppm -e 1 -m (3 for QExactive, 1 for Orbitrap) -inst (1 for QExactive, 1 for Orbitrap) -ntt 1 -thread 2 -tda 1 -ti 0,1 -n 1 -maxLength 50 -mod <file>.txt",
                "phosphosite_localization": "string",
                "ms1_data_analysis": "ProMS",
                "psm_report_generation": "single_file_report.exe",
                "cptac_dcc_mzidentml": "1.2.2",
                "mzidentml_refseq": "r82",
                "mzidentml_uniprot": "2017_06",
                "gene_to_prot": "2017-07-20",
                "cptac_galaxy_workflows": "N/A",
                "cptac_galaxy_tools": "N/A",
                "cdap_reports": "N/A",
                "cptac_dcc_tools": "N/A"
              }
            ]
          }
        }
        {} workflowMetadata
        dataworkflowMetadataDef(optional)
        {} workflowMetadataDef
        workflowMetadataarray[workflowMetadataDesc](optional)
        {} workflowMetadataDesc
        workflow_metadata_idstring(optional)
        study_idstring(optional)
        protocol_idstring(optional)
        workflow_metadata_submitter_idstring(optional)
        pdc_study_idstring(optional)
        study_submitter_idstring(optional)
        protocol_submitter_idstring(optional)
        cptac_study_idstring(optional)
        submitter_id_namestring(optional)
        study_submitter_namestring(optional)
        analytical_fractionstring(optional)
        experiment_typestring(optional)
        instrumentstring(optional)
        refseq_database_versionstring(optional)
        uniport_database_versionstring(optional)
        hgnc_versionstring(optional)
        raw_data_processingstring(optional)
        raw_data_conversionstring(optional)
        sequence_database_searchstring(optional)
        search_database_parametersstring(optional)
        phosphosite_localizationstring(optional)
        ms1_data_analysisstring(optional)
        psm_report_generationstring(optional)
        cptac_dcc_mzidentmlstring(optional)
        mzidentml_refseqstring(optional)
        mzidentml_uniprotstring(optional)
        gene_to_protstring(optional)
        cptac_galaxy_workflowsstring(optional)
        cptac_galaxy_toolsstring(optional)
        cdap_reportsstring(optional)
        cptac_dcc_toolsstring(optional)
Warning