# The Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic Targets

> **NIH NIH U24** · JOHNS HOPKINS UNIVERSITY · 2020 · $1,061,100

## Abstract

As one of the five current CPTAC PCCs, we propose to leverage our established center to further our research
in the comprehensive characterization of biospecimens from human and preclinical models for additional cancer
types. We have assembled an outstanding team of basic and clinical scientists to discover and confirm proteins
and protein modifications associated with cancer progression using genoproteomic approaches. This
multidisciplinary team will be managed by the same three Principal Investigators (PI) and consists of
internationally recognized experts in proteomic technologies, genomics, proteogenomics-specific bioinformatics,
biostatistics, oncology, pathology, cancer biology, assay development, quality control, technology optimization,
and clinical laboratory science/clinical chemistry. Our team has complementary and integrated expertise with
previous and ongoing successful collaborations. The plan is to integrate the genomics findings with proteomic
analysis (genoproteomics) and to overcome the caveats and challenges in the comprehensive understanding of
tumor biology. We believe that genomic data provides a highly valuable molecular route towards the identification
of genes and pathways that could be useful for the detection, differential diagnosis, outcome prediction and
therapeutic targets of cancer. The proteomic approaches will provide the identification of unique features that
are inherent to proteins including post-translational modifications, such as glycosylation and phosphorylation.
We propose to use the technology platform validated during the current CPTAC which is high throughput, robust
and state of the art. These technologies are proven, with the capability of generating reproducible results across
labs. We will use a two-step strategy to characterize defined sets of genomically-characterized samples. The
first step is the discovery of target proteins from both biological and clinical specimens using mass spectrometry
and affinity based technologies. The second step is the confirmation of these targets using high-throughput,
CPTAC Tier 2 analytically validated targeted assays, for example, Multiple Reaction Monitoring Mass
Spectrometry (MRM-MS). In addition, we propose to develop pilot studies for technology improvement. The goal
is to generate accurate, reproducible, sensitive, quantitative, and multiplexed assays using optimized and
standardized high-throughput technologies for the discovered targets. While this PCC application is focused on
the proteomic characterization of biological and clinical specimens, we believe that the understanding of and
expertise in proteogenomic data analysis and translation will be critical for the success of the PCC and the overall
CPTAC network. Investigators/PIs from our proposed PCC will be part of applications for the CPTAC
Proteogenomic Data Analysis (PGDAC) and Translational Research (PTCR) Centers. Collaboration and team
work are key to the success of the CPTAC program. With this ...

## Key facts

- **NIH application ID:** 9998921
- **Project number:** 5U24CA210985-05
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** DANIEL Wanyui CHAN
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $1,061,100
- **Award type:** 5
- **Project period:** 2016-09-16 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9998921

## Citation

> US National Institutes of Health, RePORTER application 9998921, The Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic Targets (5U24CA210985-05). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/9998921. Licensed CC0.

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