Jeffrey Whiteaker, Ph.D., is currently Director of Proteomics in the laboratory of Mandy Paulovich at the Fred Hutchinson Cancer Research Center in Seattle, WA. Originally from Arizona, he received a B.S. in Chemistry at the University of Arizona and obtained a PhD from the University of California at Riverside. He pursued post-doctoral research at the University of Maryland in the laboratory of Catherine Fenselau. He has been in the Pacific Northwest since 2004, where his current research focuses on using proteomic techniques to discover and validate biomarkers related to cancer. Read More
CPTAC Assay Portal: a community web-based repository for well-characterized quantitative targeted proteomics assays
A rapidly growing trend in protein quantification is using targeted mass spectrometry (MS). Although hundreds of MS-based assays have been published, the information is dispersed throughout the literature, protocols for characterization of assay performances have not been standardized, and there is currently no public database of analytically validated assays and standard operating protocols (SOPs), which are critical for standardizing and harmonizing proteomic results across the community. As a result, despite the widespread capability to perform techniques like multiple reaction monitoring (MRM) in modern proteomic facilities, the benefits of MRM have not yet been fully realized by the wider biological and clinical research communities.
To address these issues, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as a public repository of well-characterized quantitative, targeted proteomic assays. The purpose of the CPTAC Assay Portal is to facilitate widespread adoption of targeted MS assays by disseminating SOPs, reagents, and assay characterization data. A primary aim of the portal is to bring together clinicians or biologists and analytical chemists to answer hypothesis-driven questions using targeted, MS-based assays. Assay content is accessed through queries and filters, enabling investigators to find assays to proteins involved in specific cellular pathways or protein complexes, proteins whose genes map to specific chromosomal regions, or proteins associated with specified Gene Ontologies. Assays are displayed using a protein-centric view onto which the position of peptide analytes are mapped relative to features of interest, such as sequence domains, isoforms, single nucleotide polymorphisms, and post-translational modifications. Finally, detailed characterization data (linked to the portal through Panorama, https://panoramaweb.org) are available for each assay, enabling researchers to evaluate performance prior to launching the assay in their own laboratory.