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NCI Launches Proteomics Assay Portal

In a paper recently published by the journal Nature Methods, Investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) announced the launch of a proteomics Assay Portal for multiple reaction monitoring-mass spectrometry (MRM-MS) assays.  This community web-based repository for well-characterized quantitative proteomic assays currently consists of 456 unique peptide assays to 282 unique proteins and serves as a public resource of methodologies and data related to cancer associated targets.

The contributing author of the manuscript Amanda Paulovich, M.D., Ph.D. Associate Professor at the Fred Hutchinson Cancer Research Center notes that the development of the assay portal and the recent developments in targeted mass spectrometry are logical next steps in protein characterization and understanding the basis of diseases.  

“Remarkably, over a decade since the human genome was sequenced, we still have no standardized methods for quantifying the vast majority of human proteins. Currently, the research community is reliant on antiquated technologies and poorly validated affinity reagents to quantify most proteins. This contributes to the irreproducibility of preclinical research, creates tremendous financial burden on biomedical research, and renders the human proteome clinically inaccessible.  Since proteins carry out the major functions of our cells, our inability to quantify them creates a major gap in our understanding of human disease, and is a roadblock to the development of new diagnostics and therapeutics.  We hope to chip away at this roadblock by building an open-source, biologically-oriented community resource of standardized assays for quantifying proteins.”

The assay portal provides information about the setup, usefulness and sample data.  This tool should have a wide-ranging impact on cancer research as it provides the basic blueprint to develop more standardized quantitative assays in preclinical research to measure proteins and pathways of interest with reproducibility and accuracy.

A key component of the Assay Portal is also providing space where proteomics researchers can share quantitative assays with standard operating procedures and guidelines throughout the community.  As Researcher Jeff Whiteaker, Ph.D. from the Fred Hutchinson Cancer Research Center points out, "by incorporating guidelines for assay characterization, the portal takes an important step forward in enabling researchers to assess the performance of each assay. Furthermore, all the data and information for implementing the assays are available for download."

The Assay Portal also represents the application of “best practices” for targeted mass spectrometry developed during a two day-workshop held at the National Institutes of Health and published earlier this year in the journal of Molecular and Cellular Proteomics.  

“This assay portal brings together clinicians, biomedical researchers, basic biologists and analytical chemists to answer hypothesis-driven questions using targeted proteomic assays,” says Henry Rodriguez, Ph.D., M.B.A, Director of the Office of Cancer Clinical Proteomics Research.

Visit to explore the portal.