# PNNL Proteome Characterization Center

> **NIH NIH U24** · BATTELLE PACIFIC NORTHWEST LABORATORIES · 2020 · $987,941

## Abstract

PROJECT SUMMARY
The overall objective of the PNNL Proteome Characterization Center (PCC) is to integrate genomic information
with proteomic technologies to comprehensively characterize the proteome and post-translational modifications
(PTMs) as well as the functional interaction of proteins in signaling networks in cancers. As one of the PCCs in
the current Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, PNNL successfully applied
advanced proteomics capabilities and expertise to the comprehensive proteogenomic and phosphoproteomic
characterization of ovarian high-grade serous carcinomas from The Cancer Genome Atlas, and has developed
novel mass spectrometric approaches to facilitate the analysis of intact proteins, low stoichiometry PTMs, and
extremely small samples. The planned PNNL PCC will build on these achievements and contribute to the
success of the CPTAC network by characterizing multiple new tumor types assigned by CPTAC, using both
the proven standardized, multiplexed discovery and targeted confirmatory workflows as well as introducing
novel technologies and platforms, as appropriate, to improve proteomic measurements. Both human
biospecimens and preclinical models provided by NCI will be analyzed.
The Discovery Research Arm will comprehensively characterize the proteome and multiple PTM-omes in
human biospecimens and preclinical samples of 2-3 cancers with the validated advanced proteomics
platforms, integrated workflows and informatics tools, using highly multiplexed isobaric labeling and state-of-
the-art liquid chromatography-tandem mass spectrometry instrumentation at a throughput of up to 300 samples
per year. The Confirmatory Research Arm will verify the impact of genomic variation on the changes in
proteome and PTM-omes with validated targeted proteomics platforms (e.g., multiple reaction monitoring),
peptide standards and quality assurance. Up to 100 highly specific, multiplexed targeted proteomics assays for
both proteins and PTMs will be developed each year for the confirmatory studies using up to 150 samples per
year. We will also refine and validate several developmental strategies and platforms at the PNNL PCC
leveraging our on-going technology development in areas such as ultrafast gas phase separations and small-
sized sample analysis platforms and methodologies to further improve the throughput and sensitivity in both
the discovery and confirmatory studies.
The PNNL PCC will work closely with the other PCCs, Proteogenomic Data Analysis Centers and
Proteogenomic Translational Research Centers in the CPTAC network on data integration and bioinformatics
analysis, as well as translational applications.

## Key facts

- **NIH application ID:** 9997667
- **Project number:** 5U24CA210955-05
- **Recipient organization:** BATTELLE PACIFIC NORTHWEST LABORATORIES
- **Principal Investigator:** Tao Liu
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $987,941
- **Award type:** 5
- **Project period:** 2016-09-21 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9997667

## Citation

> US National Institutes of Health, RePORTER application 9997667, PNNL Proteome Characterization Center (5U24CA210955-05). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9997667. Licensed CC0.

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