Proteomic Data Commons Now Supports Metabolomics and Lipidomics Data

The National Cancer Institute's Proteomic Data Commons (PDC) launched in 2020, part of the National Cancer Institute’s Cancer Research Data Commons (CRDC) data ecosystem, is the largest public repository of comprehensive tumor proteomic datasets, housing diverse data types such as proteome, phosphoproteome, glycoproteome, acetylome, and ubiquitylome, with accompanying genomic datasets and medical images.

Aligned with its mission, the PDC has recently launched a new feature supporting the distribution of mass spectrometry-based metabolomics and lipidomics data. The study of lipids and other metabolites in biological systems allows researchers to take a “snapshot” of the physiological state of cells. These snapshots reflect real-time biochemical activity and help researchers identify metabolic vulnerabilities in cancer, which enables the discovery of new treatments. When integrated with other omes, metabolomics and lipidomics data contribute to a more complete view of tumor biology and the microenvironment.

This new feature includes raw mass spectrometry files, harmonized metadata, and any processed data provided by data submitters as supplementary data. The PDC is the first database of its kind to present metabolomics and lipidomics data along with the proteomics data from the same sample cohort.

"By integrating metabolomics and lipidomics data with existing proteomics datasets, the PDC continues to expand as a comprehensive resource," said Dr. Ratna Rajesh Thangudu, a leader at the PDC, "[The PDC] continues to offer researchers new opportunities to explore CPTAC’s multi-omics datasets within the Cancer Research Data Commons and uncover deeper insights."

See below for a summary of currently available metabolomics and lipidomics data and subscribe for CPTAC updates or to the PDC mailing list to be alerted when more data is released.

New Metabolomics and Lipidomics Studies Released

Program: Clinical Proteomic Tumor Analysis Consortium (CPTAC)

Study Name	Study ID
CPTAC CCRCC Confirmatory Study - Training - Metabolome	PDC000534
CPTAC CCRCC Confirmatory Study - Validation - Metabolome	PDC000535
CPTAC non-ccRCC Study - Metabolome	PDC000544
CPTAC GBM Confirmatory Study - Metabolome	PDC000546
CPTAC GBM Confirmatory Study - Lipidome	PDC000547
CPTAC GBM Discovery Study - Metabolome	PDC000552
CPTAC GBM Discovery Study - Lipidome	PDC000553