· This release includes 1 new publication, and the addition of a PubMed link to an existing publication. Publication information can be found at https://pdc.cancer.gov/pdc/cptac-pancancer

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· 1 Publication Supplementary Material file has been added to the following studies:

§ CPTAC GBM Confirmatory Study - Proteome (PDC000446)

§ CPTAC GBM Confirmatory Study - CompRef Proteome (PDC000447)

§ CPTAC GBM Confirmatory Study - Phosphoproteome (PDC000448)

§ CPTAC GBM Confirmatory Study - CompRef Phosphoproteome (PDC000449)

§ CPTAC GBM Confirmatory Study - Acetylome (PDC000450)

§ CPTAC GBM Confirmatory Study - CompRef Acetylome (PDC000451)

§ CPTAC GBM Confirmatory Study - Glycoproteome (PDC000454)

§ CPTAC GBM Confirmatory Study - Metabolome (PDC000546)

§ CPTAC GBM Confirmatory Study - Lipidome (PDC000547)

All of this includes 1 file and ~205MB of Data

Data Release Notes for V4.9 (April 18, 2025)

Release of additional CPTAC Pan-Cancer analysis data:

· This release includes 2 publications. Publication information can be found at https://pdc.cancer.gov/pdc/cptac-pancancer

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: Proteogenomic Translational Research Centers (PTRC)

· Includes 2 new studies:

§ PTRC Triple-negative Breast Cancer Mitotic Vulnerability Study - Proteome (PDC000579)

§ PTRC Triple-negative Breast Cancer Mitotic Vulnerability Study - Phosphoproteome (PDC000580)

All of this includes 927 files and ~190GB of Data

Data Release Notes for V4.8 (April 7, 2025)

Updates to the previously released studies:

· Program: International Cancer Proteogenome Consortium

· Project: National Cancer Center Korea

· Protein quantitation data processed for the following studies:

§ NCC iCC – Proteome (PDC000356)

§ NCC iCC – Phosphoproteome (PDC000363)

· Project: Cancer Proteogenomics Group of National Cancer Center Korea

· Protein quantitation data processed for the following studies:

§ KNCC Glioblastoma Evolution - Proteome (PDC000514)

§ KNCC Glioblastoma Evolution - Phosphoproteome (PDC000515)

· Project: International Cancer Proteogenome Consortium (ICPC): Proteogenomics of Oral Squamous Cell Carcinoma in Taiwan

· Protein quantitation data processed for the following studies:

§ CGU OSCC APOBEC3A - Proteome (PDC000519)

§ CGU OSCC APOBEC3A - Global Phosphoproteome (PDC000520)

§ CGU OSCC APOBEC3A - Multiple Phosphoproteome (PDC000521)

Data Release Notes for V4.7 (March 20, 2025)

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: Proteogenomic Translational Research Centers (PTRC)

· Includes 2 new studies:

§ PTRC BRCA CALGB40601 Neoadjuvant Trial - Proteome (PDC000582)

§ PTRC BRCA CALGB40601 Neoadjuvant Trial - Phosphoproteome (PDC000583)

All of this includes 656 files and ~103GB of Data

Data Release Notes for V4.6 (March 10, 2025)

Note: On March 11 and 12th, 2025 minor updates were pushed for some of the clinical properties for the following studies:

· Program: International Cancer Proteogenome Consortium

· Project: Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors

· Updated morphology, days_to_diagnosis and tissue_type and days_to_last_follow_up for some cases/samples in the following studies:

§ NF-PNET Discovery Study - Proteome - PhaseII (PDC000588)

§ NF-PNET Discovery Study - Phosphoproteome - PhaseII (PDC000589)

§ NF-PNET Discovery Study - Proteome - PhaseI (PDC000590)

§ NF-PNET Discovery Study - Phosphoproteome - PhaseI (PDC000591)

§ NF-PNET Validation Study - DIA (PDC000592)

New studies released:

· Program: International Cancer Proteogenome Consortium

· Project: International Cancer Proteogenome Consortium (ICPC): Proteogenomics of Oral Squamous Cell Carcinoma in Taiwan

· Includes 3 new studies:

§ CGU OSCC APOBEC3A - Proteome (PDC000519)

§ CGU OSCC APOBEC3A - Global Phosphoproteome (PDC000520)

§ CGU OSCC APOBEC3A - Multiple Phosphoproteome (PDC000521)

· Project: Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors

· Includes 5 new studies:

§ NF-PNET Discovery Study - Proteome - PhaseII (PDC000588)

§ NF-PNET Discovery Study - Phosphoproteome - PhaseII (PDC000589)

§ NF-PNET Discovery Study - Proteome - PhaseI (PDC000590)

§ NF-PNET Discovery Study - Phosphoproteome - PhaseI (PDC000591)

§ NF-PNET Validation Study - DIA (PDC000592)

· Program: Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO)

· Project: APOLLO-OV

· Includes 1 new study:

§ APOLLO-OV - Proteome (PDC000585)

All of this includes 27695 files and ~8.8TB of Data

The capitalization of certain clinical properties has been harmonized with the Data Dictionary:

· Diagnosis

· Diagnosis_is_primary_disease

· Last_known_disease_status

Update of clinical data for CPTAC studies:

Clinical data, including attributes related to patient outcome, are updated for the following cancer cohorts from the program - Clinical Proteomic Tumor Analysis Consortium. The previous CPTAC clinical data update was version 3.7.

Clear Cell Renal Cell Carcinoma

Affected Studies:

· CPTAC CCRCC Discovery Study - Proteome (PDC000127)

· CPTAC CCRCC Discovery Study – Phosphoproteome (PDC000128)

· CPTAC CCRCC Discovery Study – DIA Proteome (PDC000200)

· CPTAC CCRCC Discovery Study - Intact Glycoproteome (PDC000471)

· CPTAC CCRCC Confirmatory Study - DIA Proteome (PDC000411)

· CPTAC CCRCC Confirmatory Study - DIA Phosphoproteome (PDC000412)

· CPTAC CCRCC Confirmatory Study - DIA Intact Glycoproteome (PDC000413)

· CPTAC CCRCC Confirmatory Study - Intratumor Heterogeneity - DIA Proteome (PDC000414)

· CPTAC CCRCC Confirmatory Study - Kinase Inhibition - DIA Phosphoproteome (PDC000415)

Glioblastoma

Affected Studies:

· CPTAC GBM Discovery Study – Proteome (PDC000204)

· CPTAC GBM Discovery Study – Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study – Acetylome (PDC000245)

· CPTAC GBM Confirmatory Study - Proteome (PDC000446)

· CPTAC GBM Confirmatory Study - Phosphoproteome (PDC000448)

· CPTAC GBM Confirmatory Study - Acetylome (PDC000450)

· CPTAC GBM Confirmatory Study - Glycoproteome (PDC000454)

· CPTAC GBM Confirmatory Study - Metabolome (PDC000546)

· CPTAC GBM Confirmatory Study - Lipidome (PDC000547)

Head and Neck Squamous Cell Carcinoma

Affected Studies:

· CPTAC HNSCC Discovery Study – Proteome (PDC000221)

· CPTAC HNSCC Discovery Study – Phosphoproteome (PDC000222)

Lung Adenocarcinoma

Affected Studies:

· CPTAC LUAD Discovery Study – Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study – Proteome (PDC000150)

· CPTAC LUAD Discovery Study – Acetylome (PDC000224)

Lung Squamous Cell Carcinoma

Affected Studies:

· CPTAC LSCC Discovery Study – Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study – Acetylome (PDC000233)

· CPTAC LSCC Discovery Study – Proteome (PDC000234)

· CPTAC LSCC Discovery Study – Ubiquitylome (PDC000237)

Pancreatic Ductal Adenocarcinoma

Affected Studies:

· CPTAC PDA Discovery Study – Proteome (PDC000270)

· CPTAC PDA Discovery Study – Phosphoproteome (PDC000271)

· CPTAC PDA Discovery Study – Glycoproteome (PDC000272)

· CPTAC PDA Discovery Study – DIA Proteome (PDC000341)

· Sampling techniques for enrichment of PDAC – Proteome (PDC000393)

· CPTAC PDAC BioTExt – Proteome (PDC000504)

· CPTAC PDAC Proteins in Serum – Proteome (PDC000526)

· CPTAC PDAC Proteins in Serum – Glycoproteome (PDC000527)

Uterine Corpus Endometrial Carcinoma

Affected Studies:

· CPTAC UCEC Discovery Study – Proteome (PDC000125)

· CPTAC UCEC Discovery Study – Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study – Acetylome (PDC000226)

· CPTAC UCEC Confirmatory Study – Proteome (PDC000439)

· CPTAC UCEC Confirmatory Study – Phosphoproteome (PDC000441)

· CPTAC UCEC Confirmatory Study – Acetylome (PDC000443)

· CPTAC UCEC Confirmatory Study – Glycoproteome (PDC000445)

Note:

To download clinical data from PDC portal, identify the data of your interest by applying filters and then move to the 'Clinical' tab on the browse page. Select the checkbox to select a specific row, all rows on the page or all pages and then click the export clinical manifest button in CSV or TSV format. Clinical data are organized into multiple files and are exported as a single tar.gz archive. The clinical manifest includes data for demographic and diagnosis and the exposure manifest includes exposure related data.

Clinical data entities and properties affected by the update:

o Demographic

o Race

o Age at index

o Age is obfuscated

o Cause of death

o Days to birth

o Days to death

o Vital status

· Diagnosis

o Age at diagnosis

o Days to last follow up

o Days to last known disease status

o Days to recurrence

o Diagnosis is primary disease

o Last known disease status

o Morphology

o Primary diagnosis

o Progression or recurrence

o Site of resection or biopsy

o Tissue or organ of origin

o Tumor grade

o Tumor stage

o Ajcc clinical m

o Ajcc pathologic m

o Ajcc pathologic n

o Ajcc pathologic stage

o Ajcc pathologic t

o Ajcc staging system edition

o Classification of tumor

o Residual disease

o Tumor focality

o Year of diagnosis

· Exposure

o Alcohol history

o Alcohol intensity

o Tobacco smoking status

o Years smoked

· Sample

o Biospecimen anatomic site

o Biospecimen laterality

o Days to sample procurement

o Diagnosis pathologically confirmed

o Freezing method

o initial weight

o Method of sample procurement

o Preservation method

o Sample ordinal

o Tumor code

o Tumor code id

o Tumor descriptor

Data Release Notes for V4.5 (January 3, 2025)

Release of additional CPTAC Pan-Cancer analysis data:

· This release includes 1 publication. Publication information can be found at https://pdc.cancer.gov/pdc/cptac-pancancer

Data Release Notes for V4.4 (October 3, 2024)

Release of additional CPTAC Pan-Cancer analysis data:

· This release includes 1 publication. Publication information can be found at https://pdc.cancer.gov/pdc/cptac-pancancer

External references from PDC Cases and Studies to their counterparts in resources such as GDC, IDC, TCIA and others have been added where previously missing. In addition, the link structure of links to the Kids First portal has been updated to match their current format.

Data Release Notes for V4.3 (July 25, 2024)

The PDC gene reference table has been updated in accordance with Gencode v42. This update includes the following changes:

· Protein lists associated with each gene have been updated to include Ensemble protein identifiers.

· Certain genes have had their names changed to the most recently active gene symbol.

· A new field called “Alias” has been added. This field includes the original gene symbols for those whose names have been changed, along with other alternative names and symbols for genes.

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Publication information has been added for the following studies:

§ CPTAC GBM Confirmatory Study - Proteome (PDC000446)

§ CPTAC GBM Confirmatory Study - CompRef Proteome (PDC000447)

§ CPTAC GBM Confirmatory Study - Phosphoproteome (PDC000448)

§ CPTAC GBM Confirmatory Study - CompRef Phosphoproteome (PDC000449)

§ CPTAC GBM Confirmatory Study - Acetylome (PDC000450)

§ CPTAC GBM Confirmatory Study - CompRef Acetylome (PDC000451)

§ CPTAC GBM Confirmatory Study - Glycoproteome (PDC000454)

§ CPTAC GBM Confirmatory Study - Metabolome (PDC000546)

§ CPTAC GBM Confirmatory Study - Lipidome (PDC000547)

· Protein Quantitation data has been refreshed to ensure the unique identifiers in the heatmaps and quant files are in sync with the unique identifiers used in the study. No data has been changed, only the aliquot_run_metadata_id and study_run_metadata_id fields. This has been done for the following studies:

§ CPTAC non-ccRCC Study – Proteome (PDC000464)

§ CPTAC non-ccRCC Study – Phosphoproteome (PDC000465)

Data Release Notes for V4.2 (July 2, 2024)

Release of additional CPTAC Pan-Cancer analysis data:

· This release includes 1 publication. Publication information can be found at https://pdc.cancer.gov/pdc/cptac-pancancer

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Includes 11 new studies:

§ CPTAC GBM Confirmatory Study - Proteome (PDC000446)

§ CPTAC GBM Confirmatory Study - CompRef Proteome (PDC000447)

§ CPTAC GBM Confirmatory Study - Phosphoproteome (PDC000448)

§ CPTAC GBM Confirmatory Study - CompRef Phosphoproteome (PDC000449)

§ CPTAC GBM Confirmatory Study - Acetylome (PDC000450)

§ CPTAC GBM Confirmatory Study - CompRef Acetylome (PDC000451)

§ CPTAC GBM Confirmatory Study - Glycoproteome (PDC000454)

§ CPTAC GBM Confirmatory Study - Metabolome (PDC000546)

§ CPTAC GBM Confirmatory Study - Lipidome (PDC000547)

§ CPTAC GBM Discovery Study - Metabolome (PDC000552)

§ CPTAC GBM Discovery Study - Lipidome (PDC000553)

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Added workflow metadata for the following studies:

§ CPTAC non-ccRCC Study - Proteome (PDC000464)

§ CPTAC non-ccRCC Study - Phosphoproteome (PDC000465)

§ CPTAC non-ccRCC Study - Intact Glycoproteome (PDC000466)

· Program: Applied Proteogenomics OrganizationaL Learning and Outcomes - APOLLO

· Project: APOLLO1

· Treatment data is now available for cases from the following studies:

§ APOLLO LUAD - Proteome (PDC000434)

§ APOLLO LUAD - Phosphoproteome - TiO2 (PDC000435)

§ APOLLO LUAD - Phosphoproteome - FeNTA (PDC000436)

All of this includes 3724 files and ~790GB of Data

Data Release Notes for V4.1 (May 7, 2024)

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Added publication information for the following studies:

§ CPTAC non-ccRCC Study - Proteome (PDC000464)

§ CPTAC non-ccRCC Study - Phosphoproteome (PDC000465)

§ CPTAC non-ccRCC Study - Intact Glycoproteome (PDC000466)

§ CPTAC non-ccRCC Study - Metabolome (PDC000544)

Data Release notes for V4.0 (May 2, 2024)

Announcing a new feature in the PDC portal: the distribution of mass spectrometry-based Metabolomic and Lipidomic data generated by the CPTAC consortium! Things to know:

This data includes raw mass spectrometry files, harmonized metadata, as well as any processed data submitted by data submitters as supplementary data.
PDC does not perform bioinformatic analysis for metabolomics, so there won't be processed data from PDC Common Data Analysis Pipeline (CDAP).

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Includes 6 new studies:

§ CPTAC non-ccRCC Study - Proteome (PDC000464)

§ CPTAC non-ccRCC Study - Phosphoproteome (PDC000465)

§ CPTAC non-ccRCC Study - Intact Glycoproteome (PDC000466)

§ CPTAC CCRCC Confirmatory Study - Training - Metabolome (PDC000534)

§ CPTAC CCRCC Confirmatory Study - Validation - Metabolome (PDC000535)

§ CPTAC non-ccRCC Study - Metabolome (PDC000544)

· Project: CPTAC3-Other

· Includes 2 new studies:

§ CPTAC PDAC Proteins in Serum - Proteome (PDC000526)

§ CPTAC PDAC Proteins in Serum - Glycoproteome (PDC000527)

Updates to the previously released studies:

· Program: International Cancer Proteogenome Consortium

· Project: Cancer Proteogenomics Group of National Cancer Center Korea

· Processed Mass Spectra, Peptide Spectral Matches, Protein Assembly and Quality Metrics files were added to the following studies:

§ KNCC Glioblastoma Evolution - Proteome (PDC000514)

§ KNCC Glioblastoma Evolution - Phosphoproteome (PDC000515)

All of this includes 4545 files and ~864GB of Data

Data Release Notes for V3.8.1 (February 20, 2024)

Updates to CPTAC Pan-Cancer analysis data:

· The “Pan-cancer proteogenomics characterization of tumor immunity” manuscript has been published, and the information displayed at pdc/cptac-pancancer has been updated to reflect the full details.

Data Release Notes for V3.8 (February 9, 2024)

Release of additional CPTAC Pan-Cancer analysis data:

· This release includes 1 publication with 4 supplementary files. Note that this publication is still in-press, and will be updated once officially published. Publication information and files can be found at pdc/cptac-pancancer.

New studies released:

· Program: International Cancer Proteogenome Consortium:

· Project: Cancer Proteogenomics Group of National Cancer Center Korea

· Includes 2 new studies:

§ KNCC Glioblastoma Evolution - Proteome (PDC000514)

§ KNCC Glioblastoma Evolution - Phosphoproteome (PDC000515)

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Added publication information for the following studies:

§ Beat AML Baseline Clinical – Proteome (PDC000477)

§ Beat AML Baseline Clinical – Phosphoproteome (PDC000478)

· Added Case level cross reference to Genomic Data Commons for the following studies:

§ Beat AML Baseline Clinical – Proteome (PDC000477)

§ Beat AML Baseline Clinical – Phosphoproteome (PDC000478)

· Project: CPTAC3-Other

· Added publication information for the following study:

§ CPTAC PDAC BioTExt – Proteome (PDC000504)

All of this includes 888 files and ~3TB of Data

Replacement of supplementary files:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· CPTAC CCRCC Discovery Study – Proteome (PDC000127):

§ Supplementary file “Supplementary_Data_Proteome_DIA.tar.gz” has been replaced with “Supplementary_Data_Proteome_TMT.tar.gz”. The names of the internal folders/files have been updated to replace “DIA” with “TMT”.

· CPTAC CCRCC Discovery Study – Phosphoproteome (PDC000128):

§ Supplementary file “Supplementary_Data_Phosphoproteome_DIA.tar.gz” has been replaced with “Supplementary_Data_Phosphoproteome_TMT.tar.gz”. The names of the internal folders/files have been updated to replace “DIA” with “TMT”.

· CPTAC CCRCC Confirmatory Study - DIA Proteome (PDC000411):

§ Metabolomics sample mapping file “JHU_PCC_Manifest_ccRCC_Samples_for_Metabolomics-batch_1_data.xlsx” has been replaced with an updated version.

In an ongoing effort to harmonize PDC Data with the Data Dictionary, certain values which were not appropriate and did not conform to the list of acceptable values for their property have been modified. This includes nulling “N/A” values where appropriate, reformatting numeric strings and adding “NOS” to disease types and anatomic sites where appropriate.

Clinical data entities and properties affected by the update:

· Case

o Lost To Followup

o Disease Type

o Taxon

· Demographic

o Race

· Diagnosis

o Ajcc Clinical T

o Primary Diagnosis

o Site of Resection or Biopsy

o Tissue or Organ of Origin

· Sample

o Sample Type id

o Tumor Code

o Tumor Code id

o Sample Type

· Aliquot

o Analyte Type id

Data Release Notes for V3.7 (January 16, 2024)

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: Proteogenomic Translational Research Centers

· Includes 2 new studies:

§ Beat AML Baseline Clinical – Proteome (PDC000477)

§ Beat AML Baseline Clinical – Phosphoproteome (PDC000478)

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 - Other

· Includes 1 new study:

§ CPTAC PDAC BioTExt – Proteome (PDC000504)

· Program: International Cancer Proteogenome Consortium

· Project: National Cancer Center Korea

· Includes 2 new studies:

§ NCC iCC – Proteome (PDC000356)

§ NCC iCC – Phosphoproteome (PDC000363)

All of this includes 6080 files and ~1.35TB of Data

Update of clinical data for CPTAC studies:

Clear Cell Renal Cell Carcinoma

Affected Studies:

· CPTAC CCRCC Discovery Study - Proteome (PDC000127)

· CPTAC CCRCC Discovery Study – Phosphoproteome (PDC000128)

· CPTAC CCRCC Discovery Study – DIA Proteome (PDC000200)

· CPTAC CCRCC Discovery Study - Intact Glycoproteome (PDC000471)

· CPTAC CCRCC Confirmatory Study - DIA Proteome (PDC000411)

· CPTAC CCRCC Confirmatory Study - DIA Phosphoproteome (PDC000412)

· CPTAC CCRCC Confirmatory Study - DIA Intact Glycoproteome (PDC000413)

· CPTAC CCRCC Confirmatory Study - Intratumor Heterogeneity - DIA Proteome (PDC000414)

· CPTAC CCRCC Confirmatory Study - Kinase Inhibition - DIA Phosphoproteome (PDC000415)

Glioblastoma

Affected Studies:

· CPTAC GBM Discovery Study – Proteome (PDC000204)

· CPTAC GBM Discovery Study – Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study – Acetylome (PDC000245)

Head and Neck Squamous Cell Carcinoma

Affected Studies:

· CPTAC HNSCC Discovery Study – Proteome (PDC000221)

· CPTAC HNSCC Discovery Study – Phosphoproteome (PDC000222)

Lung Adenocarcinoma

Affected Studies:

· CPTAC LUAD Discovery Study – Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study – Proteome (PDC000150)

· CPTAC LUAD Discovery Study – Acetylome (PDC000224)

Lung Squamous Cell Carcinoma

Affected Studies:

· CPTAC LSCC Discovery Study – Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study – Acetylome (PDC000233)

· CPTAC LSCC Discovery Study – Proteome (PDC000234)

· CPTAC LSCC Discovery Study – Ubiquitylome (PDC000237)

Pancreatic Ductal Adenocarcinoma

Affected Studies:

· CPTAC PDA Discovery Study – Proteome (PDC000270)

· CPTAC PDA Discovery Study – Phosphoproteome (PDC000271)

· CPTAC PDA Discovery Study – Glycoproteome (PDC000272)

· CPTAC PDA Discovery Study – DIA Proteome (PDC000341)

· Sampling techniques for enrichment of PDAC – Proteome (PDC000393)

Uterine Corpus Endometrial Carcinoma

Affected Studies:

· CPTAC UCEC Discovery Study – Proteome (PDC000125)

· CPTAC UCEC Discovery Study – Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study – Acetylome (PDC000226)

· CPTAC UCEC Confirmatory Study – Proteome (PDC000439)

· CPTAC UCEC Confirmatory Study – Phosphoproteome (PDC000441)

· CPTAC UCEC Confirmatory Study – Acetylome (PDC000443)

· CPTAC UCEC Confirmatory Study – Glycoproteome (PDC000445)

Note:

Clinical data entities and properties affected by the update:

· Demographic

o Cause of Death

o Vital Status

o Cause of Death

o Days to Death

o Year of Death

· Diagnosis

o Age at Diagnosis

o Ajcc pathologic m

o Ajcc clinical m

o Ajcc pathologic t

o Ajcc pathologic n

o Ajcc pathologic stage

o Ajcc staging system edition

o Burkit Lymphoma Clinical Variant

o Classification of Tumor

o Days to Last Known Disease Status

o Days to Last Follow Up

o Days to Recurrence

o Last Known Disease Status

o Primary Diagnosis

o Progression or Recurrence

o Site of Resection or Biopsy

o Year of Diagnosis

· Exposure

o Alcohol History

o Alcohol Intensity

o Years Smoked

o Secondhand Smoke as Child

o Tobacco Smoking Status

o Type of Smoke exposure

o Type of Tobacco Used

· Sample

o Biospecimen Anatomic Site

o Biospecimen Laterality

o Days to Sample Procurement

o Diagnosis Pathologically Confirmed

o Freezing Method

o Initial Weight

o Longest Dimension

o Method of Sample Procurement

o Preservation Method

o Sample Ordinal

o Sample Type

o Sample Type ID

o Tissue Type

o Tumor Code

o Tumor Code ID

o Tumor Descriptor

Data Release Notes for V3.6.2 (December 14, 2023)

Updates to CPTAC Pan-Cancer analysis data:

· The supplementary file for the publication “Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation” was found to be corrupt, and the long file name was causing issues for Windows users when attempting to extract the internal files. A renamed, updated version of the file is now available to be downloaded at https://pdc.cancer.gov/pdc/cptac-pancancer

o Pan-Cancer_analysis_of_post-translational_modifications_reveals_shared_patterns_of_protein_regulation.zip has been replaced with:

o PMID_37582358_supplementary_data_v2.zip

Data Release Notes for V3.6.1 (December 7, 2023)

Updates to CPTAC Pan-Cancer analysis data:

· The file "RNA_Broad_v1.zip" in the Supplementary Information section on the Pan-Cancer page was found to be corrupt. This file has been replaced with an intact version which can be downloaded at https://pdc.cancer.gov/pdc/cptac-pancancer

Data Release Notes for V3.6 (November 16, 2023)

Updates to the previously released studies:

· Program: Applied Proteogenomics OrganizationaL Learning and Outcomes - APOLLO

· Project: APOLLO1

· Protein quantitation data processed for the following studies:

§ APOLLO LUAD - Proteome (PDC000434)

§ APOLLO LUAD - Phosphoproteome - TiO2 (PDC000435)

§ APOLLO LUAD - Phosphoproteome - FeNTA (PDC000436)

· Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Protein quantitation data processed for the following studies:

§ CPTAC UCEC Confirmatory Study – Proteome (PDC000439)

§ CPTAC UCEC Confirmatory Study – Phosphoproteome (PDC000441)

§ CPTAC UCEC Confirmatory Study – Acetylome (PDC000443)

Updates:

In an ongoing effort to harmonize PDC Data with the Data Dictionary, the capitalization of characters in certain values has been modified to match how they appear in the list of acceptable values in the Data Dictionary. For example, all Taxon values which were previously “Homo Sapiens” have been changed to “Homo sapiens”.

Clinical data entities and properties affected by the update:

· Case

o Taxon

· Demographic

o Ethnicity

o Sex

o Race

o Vital Status

· Diagnosis

o Last Known Disease Status

o Primary Diagnosis

o Site of Resection or Biopsy

o Tissue or Organ of Origin

o Prior Malignancy

o Progression or Recurrence

· Exposure

o Type of Smoke Exposure

· Sample

o Pool

o Tissue Type

o Sample is Ref

· Aliquot

o Analyte Type

o Aliquot Is Ref

Data Release Notes for V3.5 (September 4, 2023)

Release of additional CPTAC Pan-Cancer analysis data:

· This release includes 1 publication. Publication information can be found at https://pdc.cancer.gov/pdc/cptac-pancancer

· PubMed links for this and the 5 previously released publications have been added.

Data Release Notes for V3.4 (August 15, 2023)

Release of additional CPTAC Pan-Cancer analysis data:

· This release includes 5 publications, 2 of which have downloadable publication supplementary material. Publication information and files can be found at https://pdc.cancer.gov/pdc/cptac-pancancer

Data Release Notes for V3.3 (August 10, 2023)

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Includes 7 new studies:

§ CPTAC UCEC Confirmatory Study – Proteome (PDC000439)

§ CPTAC UCEC Confirmatory Study – CompRef Proteome (PDC000440)

§ CPTAC UCEC Confirmatory Study – Phosphoproteome (PDC000441)

§ CPTAC UCEC Confirmatory Study – CompRef Phosphoproteome (PDC000442)

§ CPTAC UCEC Confirmatory Study – Acetylome (PDC000443)

§ CPTAC UCEC Confirmatory Study – CompRef Acetylome (PDC000444)

§ CPTAC UCEC Confirmatory Study – Glycoproteome (PDC000445)

All of this includes 3503 Files and ~890GB of Data

Data Release Notes for V3.2 (August 3, 2023)

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: Proteogenomic Translational Research Centers

· Includes 6 new studies:

§ PTRC HGSOC FFPE Validation – Phosphoproteome (PDC000357)

§ PTRC HGSOC FFPE Validation – Proteome (PDC000358)

§ PTRC HGSOC FFPE Discovery – Phosphoproteome (PDC000359)

§ PTRC HGSOC FFPE Discovery – Proteome (PDC000360)

§ PTRC HGSOC Frozen Validation – Phosphoproteome (PDC000361)

§ PTRC HGSOC Frozen Validation – Proteome (PDC000362)

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Publication supplementary material file “Supplementary_Processed_Genomic_Transcriptomic_Data_for_PMID-36563681.zip” was added to the following studies:

§ CPTAC CCRCC Confirmatory Study - DIA Proteome (PDC000411)

§ CPTAC CCRCC Confirmatory Study - DIA Phosphoproteome (PDC000412)

§ CPTAC CCRCC Confirmatory Study - DIA Intact Glycoproteome (PDC000413)

§ CPTAC CCRCC Confirmatory Study - Intratumor Heterogeneity - DIA Proteome (PDC000414)

§ CPTAC CCRCC Confirmatory Study - Kinase Inhibition - DIA Phosphoproteome (PDC000415)

External references to the Imaging Data Commons (IDC) have been added to studies involving the following cohorts.

· Program: Clinical Proteomic Tumor Analysis Consortium

· Breast Invasive Carcinoma (BRCA), Ovarian Serious Cystadenocarcinoma (OV), clear cell Renal Cell Carcinoma (ccRCC), Lung Adenocarcinoma (LUAD), Lung Squamous Cell Carcinoma (LSCC), Head and Neck Squamous Cell Carcinoma (HNSCC), Glioblastoma (GBM), Uterine Corpus Endometrial Carcinoma (UCEC)

All of this includes 3507 Files and ~1.7TB of Data

Data Release Notes for V3.1 (June 29, 2023)

Release of additional CPTAC Pan-Cancer analysis data:

· This release includes 16 files. Those included in this release are open-access genomic data files and clinical/other metadata files. Files can be found and downloaded at https://pdc.cancer.gov/pdc/cptac-pancancer

· No publications are included in this release. Publication information will be made available as they are published.

External references to The Cancer Imaging Archive (TCIA) have been updated. In addition, case-level references to TCIA for the following cohorts have been added.

· Program: Clinical Proteomic Tumor Analysis Consortium

· Breast Invasive Carcinoma (BRCA), Ovarian Serious Cystadenocarcinoma (OV), clear cell Renal Cell Carcinoma (ccRCC)

Data Release Notes for V3.0 (May 4, 2023)

Release of CPTAC Pan-Cancer analysis data:

A new CPTAC Pan-Cancer Analysis Page has been set up to provide information on the data generated by the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC), which includes large-scale proteomic and genomic analysis of prevalent types of cancer to aid in cancer research. The page offers access to papers analyzing the data, links to the data itself, and supplementary materials from these publications.

· This release includes a total of 13 files. Files can be found and downloaded at https://pdc.cancer.gov/pdc/cptac-pancancer

· No publications are included in this release. Publication information will be made available as they are published.

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Added publication information for the following study:

§ CPTAC CCRCC Discovery Study - Intact Glycoproteome (PDC000471)

· Program: Applied Proteogenomics OrganizationaL Learning and Outcomes - APOLLO

· Project: APOLLO1

· Added Case level cross reference to Genomic Data Commons for the following studies:

§ APOLLO LUAD - Proteome (PDC000434)

§ APOLLO LUAD - Phosphoproteome - TiO2 (PDC000435)

§ APOLLO LUAD - Phosphoproteome - FeNTA (PDC000436)

Correction:

Updated the sample to aliquot mapping for the following aliquots of the case: C3N-01405:

· "CPT0105330003" is now mapped to tumor sample "C3N-01405-01", whereas it was previously mapped to solid tissue normal samples "C3N-01405-06, C3N-01405-07".

· "CPT0105370004" is now mapped to solid tissue normal samples "C3N-01405-06, C3N-01405-07", whereas it was previously mapped to tumor sample "C3N-01405-01".

Affected studies:

· CPTAC LUAD Discovery Study – Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study – Proteome (PDC000153)

· CPTAC LUAD Discovery Study – Acetylome (PDC000224)

Data Release Notes for V2.18 (March 23, 2023)

Updates to the previously released studies:

· Program: International Cancer Proteogenome Consortium

· Project: Proteogenomics Analysis to Develop Precision Medicine for Treatment-Resistant Pancreatic Cancer

· Updated the disease type of all cases previously annotated with Pancreatic Adenocarcinoma to Pancreatic Ductal Adenocarcinoma

· Added publication information for the following studies:

§ KU PDAC Discovery Study - Global proteome (PDC000248)

§ KU PDAC Discovery Study - Phosphoproteome (PDC000249)

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Includes 1 new study:

§ CPTAC CCRCC Discovery Study - Intact Glycoproteome (PDC000471)

All of this includes 600 files and ~ 125GB of Data

Data Release Notes for V2.17 (March 9, 2023)

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Updated study description for the following studies:

§ CPTAC CCRCC Discovery Study - Proteome (PDC000127)

§ CPTAC CCRCC Discovery Study - Phosphoproteome (PDC000128)

§ CPTAC CCRCC Discovery Study - DIA Proteome (PDC000200)

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Publication supplementary material file “Supplementary_Processed_Proteomic_Data_for_PMID-36563681.zip” was added to the following studies:

§ CPTAC CCRCC Confirmatory Study - DIA Proteome (PDC000411)

§ CPTAC CCRCC Confirmatory Study - DIA Phosphoproteome (PDC000412)

§ CPTAC CCRCC Confirmatory Study - DIA Intact Glycoproteome (PDC000413)

§ CPTAC CCRCC Confirmatory Study - Intratumor Heterogeneity - DIA Proteome (PDC000414)

§ CPTAC CCRCC Confirmatory Study - Kinase Inhibition - DIA Phosphoproteome (PDC000415)

· Program: Applied Proteogenomics OrganizationaL Learning and Outcomes - APOLLO

· Project: APOLLO1

· Peptide Spectral Matches, Protein Assembly and Quality Metrics files were added to the following studies:

§ APOLLO LUAD - Proteome (PDC000434)

§ APOLLO LUAD - Phosphoproteome - TiO2 (PDC000435)

§ APOLLO LUAD - Phosphoproteome - FeNTA (PDC000436)

All of this includes 1824 files and ~ 82GB of Data

Data Release Notes for V2.16 (February 3, 2023)

Updated the disease type for 7 cases to Non-Clear Cell Renal Carcinoma. Previously, they were annotated as Clear Cell Renal Cell Carcinoma.

Affected Case Submitter ids:

· C3L-00359

· C3N-00313

· C3N-00435

· C3N-00492

· C3N-00832

· C3N-01175

· C3N-01180

Affected studies:

· CPTAC CCRCC Discovery Study – Proteome (PDC000127)

· CPTAC CCRCC Discovery Study – Phosphoproteome (PDC000128)

· CPTAC CCRCC Discovery Study – DIA Proteome (PDC000200)

Update of clinical data for CPTAC studies:

Clinical data, including attributes related to patient outcome, are updated for the following cancer cohorts from the program - Clinical Proteomic Tumor Analysis Consortium

Clear Cell Renal Cell Carcinoma

Affected Studies:

· CPTAC CCRCC Discovery Study – Proteome (PDC000127)

· CPTAC CCRCC Discovery Study – Phosphoproteome (PDC000128)

· CPTAC CCRCC Discovery Study – DIA Proteome (PDC000200)

· CPTAC CCRCC Confirmatory Study - DIA Proteome (PDC000411)

· CPTAC CCRCC Confirmatory Study - DIA Phosphoproteome (PDC000412)

· CPTAC CCRCC Confirmatory Study - DIA Intact Glycoproteome (PDC000413)

· CPTAC CCRCC Confirmatory Study - Intratumor Heterogeneity - DIA Proteome (PDC000414)

Glioblastoma

Affected Studies:

· CPTAC GBM Discovery Study – Proteome (PDC000204)

· CPTAC GBM Discovery Study – Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study – Acetylome (PDC000245)

Head and Neck Squamous Cell Carcinoma

Affected Studies:

· CPTAC HNSCC Discovery Study – Proteome (PDC000221)

· CPTAC HNSCC Discovery Study – Phosphoproteome (PDC000222)

Lung Adenocarcinoma

Affected Studies:

· CPTAC LUAD Discovery Study – Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study – Proteome (PDC000153)

· CPTAC LUAD Discovery Study – Acetylome (PDC000224)

Lung Squamous Cell Carcinoma

Affected Studies:

· CPTAC LSCC Discovery Study – Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study – Acetylome (PDC000233)

· CPTAC LSCC Discovery Study – Proteome (PDC000234)

· CPTAC LSCC Discovery Study – Ubiquitylome (PDC000237)

Pancreatic Ductal Adenocarcinoma

Affected Studies:

· CPTAC PDA Discovery Study – Proteome (PDC000270)

· CPTAC PDA Discovery Study – Phosphoproteome (PDC000271)

· CPTAC PDA Discovery Study – Glycoproteome (PDC000272)

· CPTAC PDA Discovery Study – DIA Proteome (PDC000341)

· Sampling techniques for enrichment of PDAC - Proteome (PDC000393)

Uterine Corpus Endometrial Carcinoma

Affected Studies:

· CPTAC UCEC Discovery Study – Proteome (PDC000125)

· CPTAC UCEC Discovery Study – Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study – Acetylome (PDC000226)

Clinical data entities and properties affected by the update:

· Demographic

o Race

o Vital Status

o Days to Birth

o Cause of Death

o Days to Death

o Year of Death

· Diagnosis

o Age at Diagnosis

o Days to Last Follow Up

o Days to Last Known Disease Status

o Days to Recurrence

o Diagnosis is Primary Disease

o Last Known Disease Status

o Progression or Recurrence

o Tumor Stage

o AJCC Pathologic Stage

o Residual Disease

o Tumor Focality

· Exposure

o Cigarettes Per Day

o Pack Years Smoked

o Tobacco Smoking Onset Year

o Tobacco Smoking Status

o Years Smoked

o Secondhand Smoke as Child

Note:

To download clinical data from the PDC portal, identify the data of your interest by applying filters and then move to the 'Clinical' tab on the browse page. Select the checkbox to select a specific row, all rows on the page, or all pages, and then click the export clinical manifest button in CSV or TSV format. Clinical data are organized into multiple files and are exported as a single tar.gz archive. The clinical manifest includes data for demographic and diagnosis, and the exposure manifest includes exposure related data.

Data Release Notes for V2.15 (December 22, 2022)

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Includes 5 new studies -

§ CPTAC CCRCC Confirmatory Study - DIA Proteome (PDC000411)

§ CPTAC CCRCC Confirmatory Study - DIA Phosphoproteome (PDC000412)

§ CPTAC CCRCC Confirmatory Study - DIA Intact Glycoproteome (PDC000413)

§ CPTAC CCRCC Confirmatory Study - Intratumor Heterogeneity - DIA Proteome (PDC000414)

§ CPTAC CCRCC Confirmatory Study - Kinase Inhibition - DIA Phosphoproteome (PDC000415)

All of this includes 749 files and ~ 1.7TB of Data

Data Release Notes for V2.14 (November 15, 2022)

New studies released:

· Program: Applied Proteogenomics OrganizationaL Learning and Outcomes - APOLLO

· Project: APOLLO1

· Includes 3 new studies -

§ APOLLO LUAD - Proteome (PDC000434)

§ APOLLO LUAD - Phosphoproteome - TiO2 (PDC000435)

§ APOLLO LUAD - Phosphoproteome - FeNTA (PDC000436)

All of this includes 601 files and ~ 638GB of Data

Data Release Notes for V2.13 (November 7, 2022)

Updates to the previously released studies:

· Program: International Cancer Proteogenome Consortium

· Project: Proteogenomics Analysis to Develop Precision Medicine for Treatment-Resistant Pancreatic Cancer

· Processed Mass Spectra, Peptide Spectral Matches, Protein Assembly and Quality Metrics files were added to the following studies:

§ KU PDAC Discovery Study - Global proteome (PDC000248)

§ KU PDAC Discovery Study - Phosphoproteome (PDC000249)

Release of version 2 for the following study:

· Program: Clinical Proteomic Tumor Analysis Consortium

o Project: CPTAC3 Discovery and Confirmatory

o Study:

§ CPTAC CCRCC Discovery Study - DIA Proteome (PDC000200)

· In this version of the study, CPTAC_CCRCC_W_JHU_20190112_LUMOS_C3L-00360_T.raw was replaced due to the sample swap, 7 additional raw files were added to the study, and the mzML files, generated with generic msconvert settings, available in version 1 are redacted in version 2 because the RAW to mzML conversion in DIA experiments require specific settings depending on the analysis being done.

New Studies released:

· Program: Broad Institute

· Project: Broad

· Includes 4 new studies -

§ Broad Institute - Medulloblastoma - Acetylome (PDC000430)

§ Broad Institute - Medulloblastoma - Phospho-tyrosine-enrichments (PDC000431)

§ Broad Institute - Medulloblastoma - Phosphoproteome (PDC000432)

§ Broad Institute - Medulloblastoma - Proteome (PDC000433)

All of this includes 2544 files and ~686GB of Data

Data Release Notes for V2.12 (October 21, 2022)

New Study released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery and Confirmatory

· Includes 1 new study -

§ Sampling techniques for enrichment of PDAC - Proteome (PDC000393)

All of this includes 307 files and ~74GB of Data

Data Release Notes for V2.11 (October 6, 2022)

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: Proteogenomic Translational Research Centers (PTRC)

· Peptide Spectral Matches, Protein Assembly and Quality Metrics files were added to the following studies:

§ PTRC TNBC - Proteome (PDC000408)

§ PTRC TNBC - Phosphoproteome (PDC000409)

§ PTRC TNBC PDX - Proteome (PDC000410)

New Studies released:

· Program: International Cancer Proteogenome Consortium

· Project: Proteogenomics Analysis to Develop Precision Medicine for Treatment-Resistant Pancreatic Cancer

· Includes 2 new studies -

§ KU PDAC Discovery Study - Global proteome (PDC000248)

§ KU PDAC Discovery Study - Phosphoproteome (PDC000249)

All of this includes 1567 files and ~3TB of Data

Data Release Notes for V2.10 (August 24, 2022)

New Studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: Proteogenomic Translational Research Centers (PTRC)

· Includes 3 new studies -

§ PTRC TNBC - Proteome (PDC000408)

§ PTRC TNBC - Phosphoproteome (PDC000409)

§ PTRC TNBC PDX - Proteome (PDC000410)

All of this includes 263 files and ~140GB of Data

Data Release Notes for V2.9 (July 29, 2022)

Updates to the previously released studies:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC2 Confirmatory

· The file ‘CPTAC_Colon_Cancer_Prospective_Collection_Clinical_Data_S037.xls’ has been retracted from and the file ‘CPTAC_Colon_Cancer_Prospective_Collection_Clinical_Data_S037-r2.xlsx’ has been added to the following studies

§ Prospective Colon VU Proteome (PDC000109)

§ Prospective Colon PNNL Proteome Qeplus (PDC000116)

§ Prospective Colon PNNL Phosphoproteome Lumos (PDC000117)

· The file ‘S039_BRCA_propective_clinical_data_r1.xlsx’ has been retracted from and the file ‘S039_BRCA_prospective_clinical_data_r2.xlsx’ has been added to the following studies

§ Prospective Breast BI Proteome (PDC000120)

§ Prospective Breast BI Phosphoproteome (PDC000121)

§ Prospective Breast BI Acetylome (PDC000239)

New Studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: Proteogenomic Translational Research Centers (PTRC)

· Includes 6 new studies -

§ AML Ex Vivo Drug Response: Primary Cohort - Proteome (PDC000398)

§ AML Ex Vivo Drug Response: Primary Cohort - Phosphoproteome (PDC000399)

§ AML Ex Vivo Drug Response: Sorafenib Treatment - Proteome (PDC000400)

§ AML Ex Vivo Drug Response: Sorafenib Treatment - Phosphoproteome (PDC000401)

§ AML Ex Vivo Drug Response: Combination Treatment - Proteome (PDC000402)

§ AML Ex Vivo Drug Response: Combination Treatment - Phosphoproteome (PDC000403)

All of this includes 579 files and ~ 170GB of Data

Data Release Notes for V2.8 (June 16, 2022)

Updates to the previously released studies:

· Program: Pediatric Brain Tumor Atlas - CBTN

· Project: Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study

· Diagnosis to Sample mapping data is now available for the following studies

§ Pediatric Brain Cancer Pilot Study - Proteome (PDC000180)

§ Pediatric Brain Cancer Pilot Study - Phosphoproteome (PDC000176)

Note: For cases with multiple diagnosis, a mapping of each diagnosis record to a specific sample from the case is available in a new column named ‘Related Entities’ in the clinical manifest. This information is also displayed in the clinical tab of the PDC Explore page.

Data Release Notes for V2.7 (March 10, 2022)

Updates to the previously released studies:

· Program: International Cancer Proteogenome Consortium

· Project: Academia Sinica LUAD-100

· Protein quantitation data processed and heatmaps are now available for the following studies

· Academia Sinica LUAD100-Phosphoproteome (PDC000220)

· Academia Sinica LUAD100-Proteome v2 (PDC000219)

· Peptide Spectral Matches, Protein Assembly and Quality Metrics files were added to the following studies:

· Academia Sinica LUAD100-Phosphoproteome (PDC000220)

· Academia Sinica LUAD100-Proteome v2 (PDC000219)

All of this includes 3599 files and ~30GB of Data

Data Release Notes for V2.6 (January 27, 2022)

Note: DB V2.4 and V2.5 are minor internal releases that are combined with the public release DB V2.6

Updates:

· Updates to the PDC submission template

· Added new worksheets for entities Follow-Up, Family History and Treatment

· Added and removed properties from entities as part of synchronization of PDC and GDC data dictionaries

· Reorganized properties to match the data dictionary order

New Studies released:

· Program : Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3-Other

· Includes 1 new study -

· CPTAC Deep Proteomics 2D-DIA

All of this includes 16 files and ~48 GB of Data

Addition of clinical follow-up data for CPTAC studies:

Data for the clinical entity ‘Follow-Up’ has been added to the following cancer cohorts for the program - Clinical Proteomic Tumor Analysis Consortium

Clear Cell Renal Cell Carcinoma

Affected Studies:

· CPTAC CCRCC Discovery Study - Proteome (PDC000127)

· CPTAC CCRCC Discovery Study – Phosphoproteome (PDC000128)

· CPTAC CCRCC Discovery Study – DIA Proteome (PDC000200)

Glioblastoma

Affected Studies:

· CPTAC GBM Discovery Study – Proteome (PDC000204)

· CPTAC GBM Discovery Study – Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study – Acetylome (PDC000245)

Head and Neck Squamous Cell Carcinoma

Affected Studies:

· CPTAC HNSCC Discovery Study – Proteome (PDC000221)

· CPTAC HNSCC Discovery Study – Phosphoproteome (PDC000222)

Lung Adenocarcinoma

Affected Studies:

· CPTAC LUAD Discovery Study – Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study – Proteome (PDC000150)

· CPTAC LUAD Discovery Study – Acetylome (PDC000224)

Lung Squamous Cell Carcinoma

Affected Studies:

· CPTAC LSCC Discovery Study – Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study – Acetylome (PDC000233)

· CPTAC LSCC Discovery Study – Proteome (PDC000234)

· CPTAC LSCC Discovery Study – Ubiquitylome (PDC000237)

Pancreatic Ductal Adenocarcinoma

Affected Studies:

· CPTAC PDA Discovery Study – Proteome (PDC000270)

· CPTAC PDA Discovery Study – Phosphoproteome (PDC000271)

· CPTAC PDA Discovery Study – Glycoproteome (PDC000272)

· CPTAC PDA Discovery Study – DIA Proteome (PDC000341)

Uterine Corpus Endometrial Carcinoma

Affected Studies:

· CPTAC UCEC Discovery Study – Proteome (PDC000125)

· CPTAC UCEC Discovery Study – Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study – Acetylome (PDC000226)

Note:

To download clinical data from PDC portal, identify the data of your interest by applying filters and then move to the 'Clinical' tab on the browse page. Select the checkbox to select a specific row, all rows on the page or all pages and then click the export clinical manifest button in CSV or TSV format. Clinical data are organized into multiple files and are exported as a single tar.gz archive. The clinical manifest includes data for demographic and diagnosis, the exposure manifest includes exposure related data, and the follow-up manifest includes outcome related data

Data Release Notes for V2.3 (November 24, 2021)

Updates:

· Updates to the PDC Submission template (PDC-4175 & PDC-4365)

o Added a new worksheet for entity Exposure

o Added access, downloadable, location properties to NonRaw_File_Metadadata

o Added current Data Dictionary properties to Case, Sample, Diagnosis

· Added workflow metadata for version 2 of the following studies –

o Prospective Ovarian JHU Proteome (PDC000110)

o Prospective Ovarian JHU N-linked Glycosite-containing peptide (PDC000251)

Data Release Notes for V2.2 (October 28, 2021)

Release of version 2 for the following studies

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC2 Confirmatory

· Studies:

· Prospective Ovarian JHU Proteome (PDC000110)

· In this version of the study, reporter ion label correction factors (TMT-126) were updated, CDAP analysis was re-executed for integrated decoy peptide spectrum matches, FDR-aware protein inference, and updated relative protein abundance. The raw data remains the same as in the previous version.

· Prospective Ovarian JHU N-linked Glycosite-containing peptide (PDC000251)

· In this version of the study, reporter ion label correction factors (TMT-126) were updated and CDAP Summary Reports were re-executed for updated relative glycopeptide and glycosite abundance. The raw data and peptide spectral matches remain the same as in the previous version.

All of this includes ~1000 files and ~39GB

Update of clinical data for CPTAC studies:

Clinical data, including attributes related patient outcome, are updated for the following cancer cohorts from the program - Clinical Proteomic Tumor Analysis Consortium

Clear Cell Renal Cell Carcinoma

Affected Studies:

· CPTAC CCRCC Discovery Study - Proteome (PDC000127)

· CPTAC CCRCC Discovery Study – Phosphoproteome (PDC000128)

· CPTAC CCRCC Discovery Study – DIA Proteome (PDC000200)

Glioblastoma

Affected Studies:

· CPTAC GBM Discovery Study – Proteome (PDC000204)

· CPTAC GBM Discovery Study – Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study – Acetylome (PDC000245)

Head and Neck Squamous Cell Carcinoma

Affected Studies:

· CPTAC HNSCC Discovery Study – Proteome (PDC000221)

· CPTAC HNSCC Discovery Study – Phosphoproteome (PDC000222)

Lung Adenocarcinoma

Affected Studies:

· CPTAC LUAD Discovery Study – Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study – Proteome (PDC000150)

· CPTAC LUAD Discovery Study – Acetylome (PDC000224)

Lung Squamous Cell Carcinoma

Affected Studies:

· CPTAC LSCC Discovery Study – Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study – Acetylome (PDC000233)

· CPTAC LSCC Discovery Study – Proteome (PDC000234)

· CPTAC LSCC Discovery Study – Ubiquitylome (PDC000237)

Pancreatic Ductal Adenocarcinoma

Affected Studies:

· CPTAC PDA Discovery Study – Proteome (PDC000270)

· CPTAC PDA Discovery Study – Phosphoproteome (PDC000271)

· CPTAC PDA Discovery Study – Glycoproteome (PDC000272)

· CPTAC PDA Discovery Study – DIA Proteome (PDC000341)

Uterine Corpus Endometrial Carcinoma

Affected Studies:

· CPTAC UCEC Discovery Study – Proteome (PDC000125)

· CPTAC UCEC Discovery Study – Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study – Acetylome (PDC000226)

Note:

Updates to heatmaps:

The GCT files used to display the protein quantitation data from the Common Data Analysis pipeline on the study summary pages have been updated to include additional identifiers and clinical annotations for the aliquots.

The full list of column annotations is now:

case_id

case_submitter_id

aliquot_submitter_id

aliquot_id

sample_type

aliquot_status

case_status

sample_status

disease_type

primary_site

pool

taxon

morphology

primary_diagnosis

site_of_resection_or_biopsy

tissue_or_organ_of_origin

tumor_grade

tumor_stage

icd_10_code

synchronous_malignancy

aliquot_alias

Note: Only 6 column annotations are shown by default. To display additional annotations, go to View->Options->Annotations in Morpheus menu and select the column annotation of your interest.

List of updated studies in this release:

· AML Gilteritinib Resistance - Proteome (PDC000315)

· AML Gilteritinib TimeCourse - Proteome (PDC000316)

· AML Quizartinib Resistance - Proteome (PDC000317)

· AML Gilteritinib Resistance - Phosphoproteome (PDC000318)

· AML Gilteritinib TimeCourse - Phosphoproteome (PDC000319)

· AML Quizartinib Resistance - Phosphoproteome (PDC000320)

· Prospective Breast BI Phosphoproteome v2 (PDC000121)

Data Release Notes for V2.1.1 (October 4, 2021)

Updates to the previously released studies

· A fix was applied to correctly display the tmt_131c channel in the ‘Experimental design’ tab of the study summary page on the PDC portal for studies with experimental type -TMT 11.

Data Release Notes for V2.1 (September 24, 2021)

New Studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery

o Includes 1 new study –

§ PDC00341(CPTAC PDA Discovery Study – DIA Proteome) - Only raw data

Updates to the previously released studies

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery

· Added PubMed ID and updated study description for the following studies –

o PDC000270(CPTAC PDA Discovery Study – Proteome)

o PDC000271(CPTAC PDA Discovery Study – Phosphoproteome)

o PDC000272(CPTAC PDA Discovery Study – Intact Glycoproteome)

All of this includes 187 files and ~342GB

Data Release Notes for V2.0 (September 16, 2021)

Updates to the previously released studies

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery

· Embargo lifted for studies -

· PDC000270(CPTAC PDA Discovery Study – Proteome)

· PDC000271(CPTAC PDA Discovery Study – Phosphoproteome)

· PDC000272(CPTAC PDA Discovery Study – Intact Glycoproteome)

· Publication added for studies -

· PDC000270(CPTAC PDA Discovery Study – Proteome)

· PDC000271(CPTAC PDA Discovery Study – Phosphoproteome)

· PDC000272(CPTAC PDA Discovery Study – Intact Glycoproteome)

Release of publication supplementary material for 3 studies:

· PDC000270(CPTAC PDA Discovery Study – Proteome)

· PDC000271(CPTAC PDA Discovery Study – Phosphoproteome)

· PDC000272(CPTAC PDA Discovery Study – Intact Glycoproteome)

All of this includes 1 file and ~180MB

Data Release Notes for V1.26 (August 23, 2021)

Updates:

· Protein quantitation data processed and heatmaps are now available for the following studies

· AML Gilteritinib Resistance - Proteome : (PDC000315)

· AML Gilteritinib TimeCourse - Proteome : (PDC000316)

· AML Quizartinib Resistance - Proteome : (PDC000317)

· AML Gilteritinib Resistance - Phosphoproteome : (PDC000318)

· AML Gilteritinib TimeCourse - Phosphoproteome : (PDC000319)

· AML Quizartinib Resistance - Phosphoproteome : (PDC000320)

Data Release Notes for V1.25 (August 18, 2021)

Updates:

· Pubmed link for the publication “A proteogenomic portrait of lung squamous cell carcinoma” was added for the following studies listed below. It’s pubmed id ‘34358469’ can be used to search for the manuscript on the publication page.

· CPTAC LSCC Discovery Study - Proteome (PDC000234)

· CPTAC LSCC Discovery Study - Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study - Acetylome (PDC000233)

· CPTAC LSCC Discovery Study - Ubiquitylome (PDC000237)

· Added CPTAC external reference to S063 for the following studies:

· CPTAC LSCC Discovery Study - Proteome (PDC000234)

· CPTAC LSCC Discovery Study - Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study - Acetylome (PDC000233)

· CPTAC LSCC Discovery Study - Ubiquitylome (PDC000237)

· The Biospecimen Mapping in the following Study Summary Experimental Design was correctly assigned:

· CPTAC CCRCC Discovery Study - DIA Proteome (PDC000200)

Data Release Notes for V1.24 (August 5, 2021)

Updates:

· Embargo lifted and Publication details added for studies:

· CPTAC LSCC Discovery Study - Proteome (PDC000234)

· CPTAC LSCC Discovery Study - Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study - Acetylome (PDC000233)

· CPTAC LSCC Discovery Study - Ubiquitylome (PDC000237)

Data Release Notes for V1.23 (August 5, 2021)

Updates:

· Additional supplementary metadata added for studies:

· CPTAC LSCC Discovery Study - Proteome (PDC000234)

· CPTAC LSCC Discovery Study - Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study - Acetylome (PDC000233)

· CPTAC LSCC Discovery Study - Ubiquitylome (PDC000237)

· Added protocol values for the following studies:

· Pediatric Brain Cancer Pilot Study - Proteome (PDC000180)

· Pediatric Brain Cancer Pilot Study -Phosphoproteome (PDC000176)

· The following Cases were marked as disqualified for the following studies:

· C3L-00157, C3L-00356, C3L-00938, C3L-01247, and C3L-01253

· CPTAC UCEC Discovery Study - Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study - Proteome (PDC000125)

· CPTAC UCEC Discovery Study - Acetylome (PDC000226)

· C3L-02624 and C3N-01018

· CPTAC LSCC Discovery Study - Proteome (PDC000234)

· CPTAC LSCC Discovery Study - Phosphoproteome (PDC000232)

· CPTAC LSCC Discovery Study - Acetylome (PDC000233)

· CPTAC LSCC Discovery Study - Ubiquitylome (PDC000237)

· Checksum and/or File size correction was made to file(s) for the following data categories within the following studies:

· Data Category

· Processed Mass Spectra

· Reproducible Proteome and Phosphoproteome Workflow PNNL - Proteome (PDC000310)

· Quality Metrics

· CPTAC UCEC Discovery Study - Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study - Proteome (PDC000125)

· Protein Assembly

· CPTAC UCEC Discovery Study - Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study - Proteome (PDC000125)

Data Release Notes for V1.22 (July 26, 2021)

New Studies released:

Technology Advancement Studies -

Technology Advancement Studies include Technology Assessment Studies, System Suitability Studies, and Non-CPTAC Technology Advancement and Methodology studies that were conducted to advance Proteomic technologies. These studies are primarily from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program and their collaborators that do not conform to the PDC data model due to specialized experimental designs. The data available on this page are not actively maintained, or processed by the PDC, but are distributed here as a community resource.

The data can be accessed from the TECHNOLOGY ADVANCEMENT STUDIES section which is now available on the PDC homepage. The data for these studies is only available through this webpage. There is no API(programmatic) access.

Data Release Notes for V1.21 (July 15, 2021)

New Studies released:

Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC-Other

· Includes 6 new studies:

· Microscaled Proteogenomic Methods for Precision Oncology DP1 Clinical Trial - Proteome: (PDC000325)

· Microscaled Proteogenomic Methods for Precision Oncology PDX bulk - Proteome: (PDC000327)

· Microscaled Proteogenomic Methods for Precision Oncology PDX cores - Proteome: (PDC000329)

· Microscaled Proteogenomic Methods for Precision Oncology DP1 Clinical Trial - Phosphoproteome: (PDC000326)

· Microscaled Proteogenomic Methods for Precision Oncology PDX bulk - Phosphoproteome: (PDC000328)

· Microscaled Proteogenomic Methods for Precision Oncology PDX cores - Phosphoproteome: (PDC000330)

All of this includes ~900 files and ~140GB

Updates:

· Author list for publication citation updated for all PDC studies

· Publication link was added for the following studies:

· TCGA Breast Cancer CompRef Samples - Proteome (PDC000290)

· TCGA Breast Cancer CompRef Samples - Phosphoproteome (PDC000291)

· Study description for the following studies were changed/corrected:

· Oral Squamous Cell Carcinoma Study - Proteome (PDC00262)

· HBV-Related Hepatocellular Carcinoma - Proteome (PDC000198)

· HBV-Related Hepatocellular Carcinoma - Phosphoproteome (PDC000199)

· CPTAC UCEC Discovery Study - CompRef Phosphoproteome (PDC000123)

· CPTAC UCEC Discovery Study - CompRef Proteome (PDC000124)

· CPTAC UCEC Discovery Study - Proteome (PDC000125)

· CPTAC UCEC Discovery Study - Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study - Acetylome (PDC000226)

· CPTAC UCEC Discovery Study - CompRef Acetylome (PDC000227)

· AML Gilteritinib Resistance - Proteome : (PDC000315)

· AML Gilteritinib TimeCourse - Proteome : (PDC000316)

· AML Quizartinib Resistance - Proteome : (PDC000317)

· AML Gilteritinib Resistance - Phosphoproteome : (PDC000318)

· AML Gilteritinib TimeCourse - Phosphoproteome : (PDC000319)

· AML Quizartinib Resistance - Phosphoproteome : (PDC000320)

· Added supplementary data for the following study:

· Oral Squamous Cell Carcinoma Study - Proteome (PDC00262)

· Added external reference for the following studies:

· CPTAC UCEC Discovery Study - Proteome (PDC000125)

· CPTAC UCEC Discovery Study - Phosphoproteome (PDC000126)

· Oral Squamous Cell Carcinoma Study - Proteome (PDC000262)

· Prospective Breast BI Proteome (PDC000120)

· Prospective Breast BI Phosphoproteome (PDC000121)

· Prospective Breast BI Acetylome (PDC000239)

· Prospective Breast BI - CompRef Acetylome (PDC000240)

· Prospective Breast BI - CompRef Proteome (PDC000242)

· Prospective Breast BI - CompRef Phosphoproteome (PDC000244)

· CPTAC GBM Discovery Study - Acetylome (PDC000245)

· CPTAC GBM Discovery Study - CompRef Acetylome (PDC000246)

· CPTAC GBM Discovery Study - Proteome (PDC000204)

· CPTAC GBM Discovery Study - CompRef Proteome (PDC000203)

· CPTAC GBM Discovery Study - Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study - CompRef Phosphoproteome (PDC000206)

· TCGA Breast Cancer Proteome (PDC000173)

· TCGA Breast Cancer CompRef Samples - Proteome (PDC000290)

· TCGA Breast Cancer Phosphoproteome (PDC000174)

· TCGA Breast Cancer CompRef Samples - Phosphoproteome (PDC000291)

· Added protocol values for the following study:

· CPTAC UCEC Discovery Study - CompRef Phosphoproteome (PDC000123)

· CPTAC UCEC Discovery Study - CompRef Proteome (PDC000124)

· CPTAC UCEC Discovery Study - Proteome (PDC000125)

· CPTAC UCEC Discovery Study - Phosphoproteome (PDC000126)

· Buparlisib Treated Xenograft Tumors of TNBC - Proteome (PDC000307)

· Buparlisib Treated Xenograft Tumors of TNBC - Phosphoproteome (PDC000308)

Data Release Notes for V1.20 (June 24, 2021)

New Studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: Proteogenomic Translational Research Centers (PTRC)

· Includes 6 new studies:

· AML Gilteritinib Resistance - Proteome : (PDC000315)

· AML Gilteritinib TimeCourse - Proteome : (PDC000316)

· AML Quizartinib Resistance - Proteome : (PDC000317)

· AML Gilteritinib Resistance - Phosphoproteome : (PDC000318)

· AML Gilteritinib TimeCourse - Phosphoproteome : (PDC000319)

· AML Quizartinib Resistance - Phosphoproteome : (PDC000320)

All of this includes ~700 files and ~100GB

Updates:

· A Case and Biospeciemen qualification status was updated for the following studies:

· CPTAC LUAD Discovery Study - Proteome (PDC000153)

· CPTAC LUAD Discovery Study - Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study - Acetylome (PDC000224)

· Publication page: Abstract text for the following publication was corrected:

· Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy (pmid: 33212010)

· CDAP quality metric & protein report file data category for the following studies were changed:

· Reproducible Proteome and Phosphoproteome Workflow BI - Proteome: (PDC000309)

· Reproducible Proteome and Phosphoproteome Workflow JHU - Proteome: (PDC000311)

· Reproducible Proteome and Phosphoproteome Workflow PNNL - Proteome: (PDC000310)

· Reproducible Proteome and Phosphoproteome Workflow BI - Phosphoproteome: (PDC000312)

· Reproducible Proteome and Phosphoproteome Workflow JHU - Phosphoproteome: (PDC000313)

· Reproducible Proteome and Phosphoproteome Workflow PNNL - Phosphoproteome: (PDC000314)

· Reorganization of supplementary data for the following studies was changed:

· CPTAC UCEC Discovery Study - Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study - Proteome (PDC000125)

Data Release Notes for V1.19 (June 17, 2021)

New Studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3-Other

· Includes 6 new studies:

· Reproducible Proteome and Phosphoproteome Workflow BI - Proteome (PDC000309)

· Reproducible Proteome and Phosphoproteome Workflow JHU - Proteome (PDC000311)

· Reproducible Proteome and Phosphoproteome Workflow PNNL - Proteome (PDC000310)

· Reproducible Proteome and Phosphoproteome Workflow BI - Phosphoproteome (PDC000312)

· Reproducible Proteome and Phosphoproteome Workflow JHU - Phosphoproteome (PDC000313)

· Reproducible Proteome and Phosphoproteome Workflow PNNL - Phosphoproteome (PDC000314)

All of this includes ~1000 files and ~200GB

Updates:

· Publication page: Abstract typos for the following publications were corrected:

· Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy (pmid: 33212010)

· Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (pmid: 31675502)

· APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism (pmid: 28878238)

· Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer (pmid: 27372738)

· CDAP quality metric file data category for the following studies were changed:

· CPTAC CCRCC Discovery Study - Proteome (PDC000127)

· CPTAC CCRCC Discovery Study - Phosphoproteome (PDC000128)

· CPTAC CCRCC Discovery Study - CompRef Proteome (PDC000129)

· CPTAC CCRCC Discovery Study - CompRef Phosphoproteome (PDC000130)

· CPTAC GBM Discovery Study - Acetylome (PDC000245)

· CPTAC GBM Discovery Study - CompRef Acetylome (PDC000246)

· Supplementary data for the following studies was reorganized:

· Prospective Ovarian JHU N-linked Glycosite-containing peptide (PDC000251)

· Prospective Ovarian JHU Intact Glycoproteome (PDC000250)

· CPTAC GBM Discovery Study - CompRef Acetylome (PDC000246)

· CPTAC GBM Discovery Study - Acetylome (PDC000245)

· CPTAC LSCC Discovery Study - Ubiquitylome (PDC000237)

· CPTAC LSCC Discovery Study - Proteome (PDC000234)

· CPTAC LSCC Discovery Study - Acetylome (PDC000233)

· CPTAC LSCC Discovery Study - Phosphoproteome (PDC000232)

· CPTAC UCEC Discovery Study - Acetylome (PDC000226)

· CPTAC GBM Discovery Study - CompRef Phosphoproteome (PDC000206)

· CPTAC GBM Discovery Study - Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study - Proteome (PDC000204)

· CPTAC GBM Discovery Study - CompRef Proteome (PDC000203)

· CPTAC UCEC Discovery Study - Phosphoproteome (PDC000126)

· CPTAC UCEC Discovery Study - Proteome (PDC000125)

Data Release Notes for V1.18 (June 4, 2021)

New Studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC2-Other

· Includes 2 new studies:

· Buparlisib Treated Xenograft Tumors of TNBC - Proteome (PDC000307)

· Buparlisib Treated Xenograft Tumors of TNBC - Phosphoproteome (PDC000308)

All of this includes ~200 files and ~300GB

Updates:

· Publication and additional metadata added for studies:

· Prospective Colon VU Proteome (PDC000109)

· Prospective Colon PNNL Proteome Qeplus (PDC000116)

· Prospective Colon PNNL Phosphoproteome Lumos (PDC000117)

· Added external CPTAC reference for studies:

· CPTAC LUAD Discovery Study - Proteome (PDC000153)

· CPTAC LUAD Discovery Study - CompRef Proteome (PDC000154)

· CPTAC LUAD Discovery Study - Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study - CompRef Phosphoproteome (PDC000155)

· CPTAC LUAD Discovery Study - Acetylome (PDC000224)

· CPTAC LUAD Discovery Study - CompRef Acetylome (PDC000225)

· Supplementary data category for the following study was changed:

· TCGA Colon Cancer Proteome (PDC000111)

Data Release Notes for V1.17 (May 19, 2021)

New Studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC2 Retrospective

· Includes 2 new studies:

· Therapeutic Targets in Breast Cancer Xenografts - Proteome (PDC000303)

· Therapeutic Targets in Breast Cancer Xenografts - Phosphoproteome (PDC000304)

Updates:

· Program: International Cancer Proteogenome Consortium

· Project: Academia Sinica LUAD-100

· Includes 1 study update:

· Academia Sinica LUAD100-Proteome (PDC000219 v2)
- In this version of the study, a total of 5 raw files that were identified as low signal or corrupt in the version 1 are redacted and one new raw file was added as a replacement.

- Processed mass spectra files in mzml format are released.

· Added external study reference link for PDC000111, PDC000112, PDC000113, PDC000114, PDC000115, PDC000289, PDC000290, PDC000291, PDC000173, PDC000174, PDC000292, PDC000293, PDC000294

All of this includes ~2500 files and ~1TB

Data Release Notes for V1.16 (May 6, 2021)

New Studies released:
Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC2 Retrospective

· Includes 6 new studies:

· TCGA Ovarian CompRef Samples PNNL Phosphoproteome Velos Qexactive (PDC000294)

· TCGA Ovarian CompRef Samples PNNL Proteome (PDC000293)

· TCGA Ovarian CompRef Samples JHU Proteome (PDC000292)

· TCGA Breast Cancer CompRef Samples - Phosphoproteome (PDC000291)

· TCGA Breast Cancer CompRef Samples - Proteome (PDC000290)

· TCGA Colorectal Cancer CompRef Samples - Proteome (PDC000289)

· Project: CPTAC3-Other

· Includes 3 new studies:

· NCI-7 Cell Line Panel - Phosphoproteome (PDC000297)

· NCI-7 Cell Line Panel Experimental Application - Proteome (PDC000296)

· NCI-7 Cell Line Panel - Proteome (PDC000295)

Updates:

· Added TCIA link for PDC000111, PDC000173, PDC000174, PDC000112, PDC000113, PDC000114, PDC000115

All of this includes ~4300 files and ~0.7TB

Data Release Notes for V1.15 (April 22, 2021)

Updates:

· Orphan biospecimens that are not linked to any studies are dropped [PDC-3565]

· Missing publication for the PDC000121 v2 study added [PDC-3582]

· Statistics panel updated to count files from only the latest version of the studies [PDC-3583]

· Added TCIA link to PDC000120 and PDC000121 BRCA version 1 studies

Data Release Notes for V1.14 (April 15, 2021):

Updates:

A new study version feature is introduced in this release:

What is a study version?

PDC studies can have multiple versions. Additional versions (updates) of a study are created when the underlying data changes substantially. This may involve changes to the raw data, processed data, and/or metadata. When a new version is created, it may fall out of sync with the original publication of this data. Use of the latest version is strongly encouraged, as it commonly represents an update directly from the submitter.

· Release of version 2 for the following studies:

· Prospective Breast BI Proteome (PDC000121)

In this version of the study, the protein summary reports were regenerated using the updated TMT10 reporter ion isotopic distributions from the Thermo TMT10plex™ Certificate of Analysis. The raw data remains the same as in the previous version.

· Prospective Breast BI Phosphoproteome (PDC000122)

v2 includes replicate data for plex#2 02CPTAC_BCProspective_Phosphoproteome_BI_20160928). The replacement data were acquired earlier than the v1 data (02CPTAC_BCProspective_Phosphoproteome_BI_20170303) but had better phosphopeptide enrichment and a higher number of phosphosite identifications. For v2, only 02CPTAC_BCProspective_Phosphoproteome_BI_20160928 is included for distribution and in the CDAP results. However, it should be noted that both plex#2's for this study had low enrichment (62% and 72%) for versions 1 and 2, respectively, versus a typical yield of 90% The raw data from this version of the study is used in the final BRCA publication from the CPTAC consortium.

In this version of the study, the protein summary reports were regenerated using the updated TMT10 reporter ion isotopic distributions from the Thermo TMT10plex™ Certificate of Analysis.

Data Release Notes for V1.13 (April 1, 2021):

Updates:

· Release of additional supplementary data for the following studies:

· CPTAC GBM Discovery Study - Proteome (PDC000204)

· CPTAC GBM Discovery Study - Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study - CompRef Proteome (PDC000203)

· CPTAC GBM Discovery Study - CompRef Phosphoproteome (PDC000206)

· CPTAC GBM Discovery Study - Acetylome (PDC000245)

· CPTAC GBM Discovery Study - CompRef Acetylome (PDC000246)

· CPTAC CCRCC Discovery Study - Proteome S044-1 (PDC000127)

· CPTAC CCRCC Discovery Study - Phosphoproteome S044-2 (PDC000128)

· CPTAC CCRCC Discovery Study - CompRef Proteome S044-1 (PDC000129)

· CPTAC CCRCC Discovery Study - CompRef Phosphoproteome S044-2 (PDC000130)

· CPTAC CCRCC Discovery Study - DIA Proteome (PDC000200)

· TCGA COAD Proteome S016-1 (PDC000111)

· TCGA OV Glycoproteome S020-1 (PDC000112)

· TCGA OV Proteome S020-2 (PDC000113)

· TCGA OV Proteome S020-3 (PDC000114)

· TCGA OV Phosphoproteome S020-4 (PDC000115)

· TCGA BRCA Phosphoproteome S015-2 (PDC000174)

· TCGA BRCA Proteome S015-1 (PDC000173)

· Prospective Breast BI Acetylome (PDC000239)

· Prospective Breast BI - CompRef Acetylome (PDC000240)

· Prospective Breast Proteome S039-1 (PDC000120)

· Prospective Breast BI - CompRef Proteome (PDC000242)

· Prospective Breast Phosphoproteome S039-2 (PDC000121)

· Prospective Breast BI - CompRef Phosphoproteome (PDC000244)

· Release of additional metadata for the following studies:

· CPTAC LUAD Discovery Study - Proteome (PDC000153)

· CPTAC LUAD Discovery Study - Phosphoproteome (PDC000149)

· CPTAC LUAD Discovery Study - Acetylome (PDC000224)

· CPTAC LUAD Discovery Study - CompRef Acetylome (PDC000225)

· CPTAC LUAD Discovery Study - CompRef Proteome (PDC000154)

· CPTAC LUAD Discovery Study - CompRef Phosphoproteome (PDC000155)

· CPTAC GBM Discovery Study - Proteome (PDC000204)

· CPTAC GBM Discovery Study - Phosphoproteome (PDC000205)

· CPTAC GBM Discovery Study - CompRef Proteome (PDC000203)

· CPTAC GBM Discovery Study - CompRef Phosphoproteome (PDC000206)

· CPTAC GBM Discovery Study - Acetylome (PDC000245)

· CPTAC GBM Discovery Study - CompRef Acetylome (PDC000246)

· CPTAC CCRCC Discovery Study - Proteome S044-1 (PDC000127)

· CPTAC CCRCC Discovery Study - Phosphoproteome S044-2 (PDC000128)

· CPTAC CCRCC Discovery Study - CompRef Proteome (PDC000129)

· CPTAC CCRCC Discovery Study - CompRef Phosphoproteome (PDC000130)

· CPTAC CCRCC Discovery Study - DIA Proteome (PDC000200)

Data Release Notes for V1.12 (March 18, 2021):

Updates:

· Updated workflow metadata for the following studies (PDC-3028) -

· CPTAC GBM Discovery Study - CompRef Proteome ( PDC000203)

· CPTAC LUAD Discovery Study - CompRef Phosphoproteome (PDC000155)

· CPTAC LUAD Discovery Study - CompRef Proteome (PDC000154)

· CPTAC CCRCC Discovery Study - CompRef Phosphoproteome ( PDC000130)

· CPTAC CCRCC Discovery Study - CompRef Proteome ( PDC000129)

· CPTAC UCEC Discovery Study - CompRef Phosphoproteome( PDC000123)

· CPTAC UCEC Discovery Study - CompRef Proteome(PDC000124)

· Study PDC000278 merged with the project - CPTAC retrospective ("project_id": "48af5040-5546-11e8-b664-00a098d917f8") (PDC-3483) - March 24, 2021

Data Release Notes for V1.11 (March 10, 2021):

New Studies released:

· Program : Clinical Proteomic Tumor Analysis Consortium

· Project : CPTAC2 Retrospective

· Includes 1 new study:

· VU Normal Colon Epithelium - Proteome

All of this includes ~3600 files and ~0.5TB

Updates:

· Updates to the PDC Submission template (PDC-3399)

· Updated hyperlinks in all worksheets

· Updated contact email address in worksheet “Readme”

· Updated publication citation for -

· PDC000180(Pediatric Brain Cancer Pilot Study - Proteome)

· PDC000176(Pediatric Brain Cancer Pilot Study -Phosphoproteome)

· PDC000120(Prospective Breast BI Proteome)

· PDC000121(Prospective Breast BI Phosphoproteome)

· PDC000239(Prospective Breast BI Acetylome)

· PDC000240(Prospective Breast BI - CompRef Acetylome)

· PDC000242(Prospective Breast BI - CompRef Proteome)

· PDC000244(Prospective Breast BI - CompRef Phosphoproteome)

· Added supplementary files from the publication as supplementary data

· PDC000111 (TCGA Colon Cancer Proteome)

Data Release Notes for V1.10 (February 19, 2021):

Updates:

· Embargo lifted for studies -

· PDC000204(CPTAC GBM Discovery Study - Proteome)

· PDC000205(CPTAC GBM Discovery Study - Phosphoproteome)

· PDC000245(CPTAC GBM Discovery Study - Acetylome)

· PDC000203(CPTAC GBM Discovery Study - CompRef Proteome)

· PDC000206(CPTAC GBM Discovery Study - CompRef Phosphoproteome)

· PDC000246(CPTAC GBM Discovery Study - CompRef Acetylome)

· Publication added for studies -

· PDC000204(CPTAC GBM Discovery Study - Proteome)

· PDC000205(CPTAC GBM Discovery Study - Phosphoproteome)

· PDC000245(CPTAC GBM Discovery Study - Acetylome)

· PDC000203(CPTAC GBM Discovery Study - CompRef Proteome)

· PDC000206(CPTAC GBM Discovery Study - CompRef Phosphoproteome)

· PDC000246(CPTAC GBM Discovery Study - CompRef Acetylome)

Data Release Notes for V1.9 (February 5, 2021):

New Studies released:

Program : Clinical Proteomic Tumor Analysis Consortium

· Project : CPTAC3 Discovery

· Includes 3 new studies –

· CPTAC PDA Discovery Study – Proteome

· CPTAC PDA Discovery Study – Phosphoproteome

· CPTAC PDA Discovery Study - Intact Glycoproteome

All of this includes ~4500 files and ~1TB.

Other Updates:

· Embargo lifted for studies -

· PDC000221(CPTAC HNSCC Discovery Study - Proteome)

· PDC000222(CPTAC HNSCC Discovery Study - Phosphoproteome)

· Publication added for studies -

· PDC000221(CPTAC HNSCC Discovery Study - Proteome)

· PDC000222(CPTAC HNSCC Discovery Study - Phosphoproteome)

· Updated the enumerations for the property file_format in the NonRaw_File_Metadata worksheet of the PDC submission template (PDC-3269)

Data Release Notes for V1.8 (January 5, 2021):

New Studies released:

· Program : International Cancer Proteogenome Consortium

· Project : Oral Squamous Cell Carcinoma - Chang Gung University

· Includes 1 new study -

· Oral Squamous Cell Carcinoma Study – Proteome

· Publication added for study -

· Oral Squamous Cell Carcinoma Study – Proteome

Other Updates:

Publication added for studies -

■ Oral Squamous Cell Carcinoma Study - Proteome

■ Pediatric Brain Cancer Pilot Study - Proteome

■ Pediatric Brain Cancer Pilot Study - Phosphoproteome

■ Prospective Breast BI Proteome

■ Prospective Breast BI Phosphoproteome

■ Prospective Breast BI Acetylome

■ Prospective Breast BI - CompRef Acetylome

■ Prospective Breast BI - CompRef Proteome

■ Prospective Breast BI - CompRef Phosphoproteome

■ Prospective Ovarian JHU Intact Glycoproteome

■ Prospective Ovarian JHU N-linked Glycosite-containing peptide

■ Prospective Ovarian JHU Proteome

■ Prospective Ovarian PNNL Proteome Qeplus

■ Prospective Ovarian PNNL Phosphoproteome Lumos

Updated clinical data for CPTAC 2 studies –

■ Prospective Colon VU Proteome

■ Prospective Colon PNNL Proteome Qeplus

■ Prospective Colon PNNL Phosphoproteome Lumos

■ TCGA Breast Cancer Proteome

■ TCGA Breast Cancer Phosphoproteome

■ TCGA Colon Cancer Proteome

■ TCGA Ovarian JHU Glycoproteome

■ TCGA Ovarian JHU Proteome

■ TCGA Ovarian PNNL Proteome

■ TCGA Ovarian PNNL Phosphoproteome Velos Qexatvive

All of this includes ~3500 files and ~500 GB.

Data Release Notes for V1.7 (November 12, 2020):

New Studies released:

· Program : Clinical Proteomic Tumor Analysis Consortium

· Project : CPTAC2 Confirmatory

· Includes 6 new studies -

· Prospective Breast BI Acetylome

· Prospective Breast BI - CompRef Acetylome

· Prospective Breast BI - CompRef Proteome

· Prospective Breast BI - CompRef Phosphoproteome

· Prospective Ovarian JHU Intact Glycoproteome

· Prospective Ovarian JHU N-linked Glycosite-containing peptide

Updates to the previously released studies

· Program : Pediatric Brain Tumor Atlas - CBTTC

· Project : Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study

· Release of additional supplementary data for 2 studies -

■ Pediatric Brain Cancer Pilot Study - Proteome

■ Pediatric Brain Cancer Pilot Study - Phosphoproteome

All of this includes ~1400 files and ~350 GB.

Data Release Notes for V1.6 (October 2, 2020):

New Studies released:

· Program : Clinical Proteomic Tumor Analysis Consortium

· Project : CPTAC3 Discovery

· Includes 2 new studies -

· CPTAC GBM Discovery Study - Acetylome

· CPTAC GBM Discovery Study - CompRef Acetylome

Updates to the previously released studies

· Program : Pediatric Brain Tumor Atlas - CBTTC

· Project : Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study

· Release of additional supplementary data for 2 studies -

· Pediatric Brain Cancer Pilot Study - Proteome

· Pediatric Brain Cancer Pilot Study - Phosphoproteome

All of this includes ~300 files and ~125 GB.

Data Release Notes for V1.5 (September 11, 2020):

New Studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3 Discovery

· Includes 4 new studies -

o CPTAC LSCC Discovery Study - Proteome

o CPTAC LSCC Discovery Study - Phosphoproteome

o CPTAC LSCC Discovery Study - Acetylome

o CPTAC LSCC Discovery Study - Ubiquitylome

Updates to the previously released studies

· Project: CPTAC3 Discovery

o CPTAC UCEC Discovery Study - Proteome

o CPTAC UCEC Discovery Study - Phosphoproteome

o CPTAC UCEC Discovery Study - Acetylome

§ Additional plex added to proteome and phosphoproteome

§ Updated protein reports to include the newly added plex

§ Updated quantitation data for API access

§ Added supplementary data

· Project : CPTAC3 Discovery

· Release of supplementary data

o Pediatric Brain Cancer Pilot Study - Proteome

o Pediatric Brain Cancer Pilot Study - Phosphoproteome

o Release of supplementary data

All of this includes ~4000 files and ~1 TB.

Data Release Notes for V1.4 (August 13, 2020):

New Studies released:

· Program : Clinical Proteomic Tumor Analysis Consortium

· Project : CPTAC3 Discovery

· Includes 2 new studies -

· CPTAC UCEC Discovery Study - Acetylome

· CPTAC UCEC Discovery Study - Compref Acetylome

· Program : Georgetown Proteomics Research Program

· Project : Georgetown Lung Cancer Proteomics Study

· Includes 1 new study -

· Georgetown Lung Cancer Proteomics Study (only raw data)

Updates to the previously released studies

· Program : Clinical Proteomic Tumor Analysis Consortium

· Project : CPTAC3 Discovery

· Release of quantitation data through APIs and Updates to the protein assembly files.

· CPTAC LUAD Discovery Study - Acetylome

· CPTAC LUAD Discovery Study - Compref Acetylome

Publication added for studies:

o Academia Sinica LUAD 100-Proteome

o Academia Sinica LUAD 100-Phosphoproteome

o CPTAC LUAD Discovery Study - Proteome

o CPTAC LUAD Discovery Study - Phosphoproteome

o CPTAC LUAD Discovery Study - Acetylome

o CPTAC LUAD Discovery Study - CompRef Proteome

o CPTAC LUAD Discovery Study - CompRef Phosphoproteome

o CPTAC LUAD Discovery Study - CompRef Acetylome

o CPTAC UCEC Discovery Study - Proteome

o CPTAC UCEC Discovery Study - Phosphoproteome

o CPTAC UCEC Discovery Study - Acetylome

o CPTAC UCEC Discovery Study - CompRef Proteome

o CPTAC UCEC Discovery Study - CompRef Phosphoproteome

o CPTAC UCEC Discovery Study - CompRef Acetylome

All of this includes ~500 files and ~110 GB.

Data Release Notes for V1.3 (July 8, 2020):

New studies released:

· Program: Clinical Proteomic Tumor Analysis Consortium

· Project: CPTAC3-Discovery

· Includes 2 new studies -

· CPTAC LUAD Discovery Study – Acetylome

· CPTAC LUAD Discovery Study – CompRef Acetylome

All of this includes 491 files.

Data Release Notes for V1.2 (May 13, 2020):

New Studies released:

· Program: International Cancer Proteogenomic Consortium

· Project: Academia Sinica Early Stage Non-smoking Lung Adenocarcinoma

· Includes 2 new studies:

· Academia Sinica LUAD100-Phosphoproteome

· Academia Sinica LUAD100-Proteome

· Program: CPTAC program Head and Neck Squamous Cell Carcinoma (HNSCC)

· Project: CPTAC3-Discovery

· Includes 2 new studies:

· CPTAC HNSCC Discovery Study - Phosphoproteome

· CPTAC HNSCC Discovery Study - Proteome

Data Release Notes for V1.1 (April 16, 2020):

New Studies released:

· Program : International Cancer Proteogenome Consortium

· Project : Human Early-Onset Gastric Cancer - Korea University

· Includes 3 new studies -

· Proteogenomics of Gastric Cancer - Proteom

· Proteogenomics of Gastric Cancer - Phosphoproteome

· Proteogenomics of Gastric Cancer - Glycoproteome

All of this includes 10,943 files and ~8 TB of data.