University of Victoria, CPTAC Partner
News Aug 30, 2016
University of Victoria Genome British Columbia Proteomics Centre has partnered with the U.S. National Cancer Institute (NCI) to make targeted proteomic assays accessible to the community through NCI’s CPTAC Assay Portal (https://assays.cancer.gov/). A key aspect of the Assay Portal is to provide space where national and international proteomics researchers from across the globe can upload and share their quantitative assays with standard operating procedures and guidelines.
To meet this goal, NCI is continuing to improve the assay upload process to have an independent process for public/non-CPTAC teams to upload their assays in a seamless fashion and will provide update on this effort to the community as it comes available. Targeted proteomic assays eliminate issues that are commonly observed using conventional protein detection systems (e.g. Western blotting), which are semi-quantitative at best, not readily multiplexed, and often non-specific.
Until recently, non-standardized information for hundreds of targeted mass spectrometry-based assays was distributed across published journal articles. The CPTAC assay portal serves as a centralized public repository of highly characterized targeted MS assays, including standard operating protocols, reagents, and assay characterization data.
Dr. Christoph Borchers, Ph.D., Director of the University of Victoria Genome BC Proteomics Centre, Canada, has volunteered to be the first non-CPTAC researcher to upload targeted mass spectrometry-based assays to the portal. These multiple reaction monitoring (MRM-MS)-based assays fully adhere to the standards and guidelines developed by CPTAC and meet the minimum characterization requirements for entry to the portal, including development of multipoint response curve and repeatability assessment.
In the portal landing page, which is designed to be relevant to biologists, researchers will be able to search for the Proteomics Centre assays by querying using the “non-CPTAC” term. Dr. Borchers has contributed 107 MRM assays to the portal in this initial phase, and is working on completing up to 2,000 assays that will be ultimately imported to the CPTAC Assay Portal. “We are delighted to be working with the CPTAC on this important project,” says Dr. Borchers.
“Standardization of protein quantitation is essential if mass spectrometry-based proteomics is going to be used for clinical assays. To assist in cancer-related research, we are planning to greatly extend the range of our MRM based assays in CPTAC to include assays for mouse proteins. The mouse is the preferred animal model for studying cancer, and will become even more important through the new CRISPR/Cas9 technology, which greatly facilitates the research of genetic mutations of cancer-related proteins in mice at a low cost.”
Dr. Amanda Paulovich, a Member of the Fred Hutchinson Cancer Research Center and co-Chair of the CPTAC Assay Development Working Group, notes that, “We are excited to take this important first step in opening up the Assay Portal for contributions from the entire community, bringing us one step closer to the goal of standardizing quantification of all proteins across the community to improve analytical rigor and reproducibility in protein-based research.”
Scientists have developed a way to identify the beginning of every gene — known as a translation start site or a start codon — in bacterial cell DNA with a single experiment and, through this method, they have shown that an individual gene is capable of coding for more than one protein.