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CPTAC, University of Victoria Working to Expand Targeted Proteomics Assay Portal

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NEW YORK (GenomeWeb) – The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) is partnering with the University of Victoria Genome British Columbia Proteomics Centre to develop targeted proteomics assays.

The collaboration aims to up the number of multiple reaction-monitoring assays in CPTAC's Assay Portal, which makes well-validated MRM mass spec assays available to the research community. More generally, said Christoph Borchers, director of the Proteomics Centre, it is part of a broader effort to improve the accessibility and drive use of MRM mass spec for targeted protein quantitation.

CPTAC's Assay Portal is one of several proteomics resources pursuing this aim. For instance, last week, GenomeWeb reported on the most recent release of the SRMAtlas, a collection of targeted mass spec assays developed by the Institute for Systems Biology and the Swiss Federal Institute of Technology Zurich.

That resource contains data on 166,174 proteotypic peptides and allows for quantification of 20,123 of the 20,203 annotated human proteins in the UniProtKB/Swiss-Prot database, as well as several thousand protein isoforms and post-translational modifications. It provides researchers interested in developing assays to a particular protein with information on the peptides and transitions they can use.

The CPTAC Assay Portal is less comprehensive in terms of coverage, currently offering around 900 assays, but these assays have all undergone rigorous analytical validation measuring things like limits of detection and quantitation, linearity, and reproducibility, and include detailed protocols instructing researchers on how to best implement them.

"SRMAtlas is very useful if you want to develop an assay. It is a great starting point," Borchers said. "But that is just the beginning," he added, noting that performing the required analytical validation and developing protocols for MRM assays "is a huge amount of work."

"There are a lot of MRM assays around, but they haven't all been developed [to the standard of the CPTAC Assay Portal] because it takes time and effort and money," Borchers said. "But it is important not to cut corners, but [to ensure] that these [assays] are rigorously developed and that we are presenting results that are reproducible and accurate."

He noted as well that there are many well-developed, thoroughly validated MRM assays out there, but that they are not necessarily accessible to the larger community. One of the ultimate goals of the CPTAC Assay Portal is to provide a resource for collecting these assays.

"There is [MRM development] work that has been done in many labs, and I think it is quite important to link it all together," he said. "So that the biologist who wants to quantify a protein in a particular biospecimen can go to a web page and see who has developed an MRM assay for their protein of interest and know that it will have a certain level of quality."

The CPTAC-University of Victoria partnership is the first step in that direction, with Borchers being the first researcher outside the CPTAC consortium to add assays to the portal. Borchers has considerable experience with MRM development, both through his position heading the Proteomics Centre and as co-founder and chief scientific officer of the firm MRM Proteomics, which develops and sells MRM assay kits for protein quantitation.

Thus far, Borchers and his colleagues have contributed around 100 assays to the portal, and they will ultimately add roughly 2,000 assays. Many of these assays will be to mouse proteins, which Borchers noted is an area of interest for his lab.

MRM assays to targets in mouse "is of great interest to the community," Borchers said, due to the low sample requirements of MRM mass spec compared to conventional immunoassays. Because mice have relatively small amounts of blood, researchers are limited in the number of immunoassays they can perform per animal, he said, adding that MRM mass spec allows for much higher levels of multiplexing.

"It is hard to multiplex ELISA, because you need like 20 to 200 microliters of plasma for each assay," Borchers said. Using MRM mass spec, Borchers and his colleagues can measure around 200 proteins in 20 microliters of plasma.

"So this is a huge advantage of this technology," he said.

The ability to do large multiplexes from small amounts of sample could help with a variety of experiments, Borchers noted, citing, for example, highly multiplexed, longitudinal protein measurements from a single animal. He also highlighted researchers' interested in assessing mouse phenotypes after they have undergone CRISPR/Cas9 gene editing.

"People are asking, what kind of changes do we introduce into the mouse proteome, and I think these MRM assays we are developing could be useful for scientists who want to phenotype their mouse after the gene editing," he said.

As with MRM assays in general, many MRM assays to mouse proteins exist, but not all are well-validated and they are not collected in a single, easily accessible resource, Borchers said. He said that he and his colleagues have received a funding award to support their mouse MRM development work but that he is not yet able to make the details public.

Borchers said he hoped the next step in the evolution of the CPTAC Assay Portal would be the involvement of private companies who could take the assays in the portal and make them available as kits on a large scale. He noted that MRM Proteomics offers such kits, but only a limited selection.

"You have the portal [with assays] that are fully developed, and you can take them and [implement] them yourself," he said. But even better "would be to have kits that can be easily purchased by the community."

This, he suggested, would be key to broadening MRM mass spec's appeal beyond the proteomics community.

"Biologists and clinicians and the medical community could buy the kit and go to their proteomics center and run the assay," he said. "I think this is the next step."