PDC Data

Currently available release on the CGC

February 2022 - PDC data on the CGC has been updated to match the following PDC Data Release:

V2.6 (January 27, 2021)

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)

Update history

November 2021 - PDC data on the CGC has been updated to match the following PDC Data Release:

V2.1 (September 24, 2021)

New Studies released:

Program: Clinical Proteomic Tumor Analysis Consortium
Project: CPTAC3 Discovery
- 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 –
- PDC000270(CPTAC PDA Discovery Study – Proteome)
- PDC000271(CPTAC PDA Discovery Study – Phosphoproteome)
- PDC000272(CPTAC PDA Discovery Study – Intact Glycoproteome)

September 2021 - PDC data on the CGC has been updated with the following PDC Data Releases:

July 2021 - PDC data on the CGC has been updated with the following PDC Data Release:

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

This release also includes a number of updates listed in detail in PDC Data Release Notes.

July 2021 - PDC data on the CGC has been updated with the following PDC Data Release:

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

This release also includes a number of updates listed in detail in PDC Data Release Notes.

April 2021 - PDC data on the CGC has been updated with the following PDC Data Release:

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

February 2021 - PDC data on the CGC has been updated with the following PDC Data Releases:

V1.0.24 (February 5, 2021)
V1.0.22 (January 5, 2021)
V1.0.21 (December 15, 2020)

PDC Data Release of 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.

PDC Data Release of 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

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

PDC Data Release of December 15, 2020

Update clinical data for CPTAC 2 studies (PDC-2918)

November 2020 - PDC data on the CGC has been updated to match the PDC Data Release of November 12, 2020

Release details:

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 -
• Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Proteome
• Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Phosphoproteome
All of this includes ~1400 files and ~350 GB.

October 2020 - PDC data on the CGC has been updated to match the following PDC Data Releases:

V1.0.16 (October 2, 2020)
V1.0.14 (September 11, 2020)
V1.0.12 (August 13, 2020)
V1.0.10 (July 8, 2020)

Release details:

PDC Data Release V1.0.16 (October 2, 2020):
New Studies released:

CPTAC GBM Discovery Study - Acetylome
CPTAC GBM Discovery Study - CompRef Acetylome

Updated studies:

Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Proteome
Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study – Phosphoproteome

PDC Data Release V1.0.14 (September 11, 2020):
New Studies released:

CPTAC LSCC Discovery Study - Proteome
CPTAC LSCC Discovery Study - Phosphoproteome
CPTAC LSCC Discovery Study - Acetylome
CPTAC LSCC Discovery Study - Ubiquitylome

Updated studies:

CPTAC UCEC Discovery Study - Proteome
CPTAC UCEC Discovery Study - Phosphoproteome
CPTAC UCEC Discovery Study - Acetylome
Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Proteome
Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Phosphoproteome

PDC Data Release V1.0.12 (August 13, 2020):
New Studies released:

CPTAC UCEC Discovery Study - Acetylome
CPTAC UCEC Discovery Study - Compref Acetylome
Georgetown Lung Cancer Proteomics Study (only raw data)

Updated studies:

CPTAC LUAD Discovery Study - Acetylome
CPTAC LUAD Discovery Study - Compref Acetylome

PDC Data Release V1.0.10 (July 8, 2020):
New Studies released:

CPTAC LUAD Discovery Study – Acetylome
CPTAC LUAD Discovery Study – CompRef Acetylome

July 2020 - PDC data on the CGC has been updated to match the PDC Data Releases of May 13 and June 3, 2020. Studies released:

Academia Sinica LUAD100 - Proteome
Academia Sinica LUAD100 - Phosphoproteome
CPTAC HNSCC Discovery Study - Proteome
CPTAC HNSCC Discovery Study - Phosphoproteome
CPTAC CCRCC Discovery Study - DIA Proteome

May 2020 - PDC data on the CGC has been updated to match the PDC Data Release of April 16, 2019. Studies released:

Proteogenomics of Gastric Cancer - Proteome
Proteogenomics of Gastric Cancer - Phosphoproteome
Proteogenomics of Gastric Cancer - Glycoproteome

February 2020 - PDC data on the CGC has been updated to match the PDC Data Release of December 20, 2019. Studies released:

CPTAC GBM Discovery Study - Proteome
CPTAC GBM Discovery Study - Phosphoproteome
CPTAC GBM Discovery Study - CompRef Proteome
CPTAC GBM Discovery Study - CompRef Phosphoproteome

December 2019 - PDC data on the CGC updated with the following PDC releases:

International Cancer Proteogenomic Consortium - Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma data, December 2019.
Pediatric Brain Tumor Atlas - CBTTC program Pediatric/AYA brain tumor dataset, November 2019.

October 2019 - Version of PDC data on the CGC updated to the PDC release of September 2019 (release of CPTAC3 program Lung Adenocarcinoma (LUAD) dataset)

August 2019 - The initial version of PDC data available on the CGC corresponds to the August 2019 release - Proteomic data commons for multiomic data analysis.