As far as shotgun proteomics is concerned, it’s an approach that’s had a “fantastic impact on cell biology,” said Daniel Liebler, director of the proteomics lab at the Mass Spectrometry Research Center at Vanderbilt University. “But it hasn’t really hit clinical proteomics because it’s hard to do it a high-throughput standardized way.”
But armed with a $7.5 million award from the National Cancer Institute, Liebler will be looking at ways to reengineer the shotgun approach to reduce variability in the results, and in the process increase the throughput.
This week, Liebler’s team at Vanderbilt was named one of five teams that will share $35.5 million over five years from the NCI to evaluate and test proteomic technologies applicable for cancer research.
The awards were given as part of the Clinical Proteomic Technologies Initiative for Cancer, a five-year, $104 million program started last year to assess the use of proteomic tools and data resources for cancer research. This component of the CPTI is known as the Clinical Proteomic Technology Assessment for Cancer.
In addition to Liebler’s team at Vanderbilt University, other CPTAC program award winners include teams at the Broad Institute of the Massachusetts Institute of Technology and Harvard University, which will develop mass spectrometry-based assays to detect and quantify protein biomarkers believed to be involved in cancer, particularly breast cancer; the University of California, San Francisco/Lawrence Berkeley National Laboratory, which will look to develop antibodies to proteins that exist in cancer and then use mass spectrometry to study them; Perdue University, which will look at ways of simplifying samples before mass spec examination by liquid chromatography, ion mobility, use of antibodies and use of immunological arrays; and Memorial Sloan-Kettering Cancer Center, which will try to develop cancer diagnostic tools that measure breakdown products in blood such as protein fragments.
Additionally, CPTI also announced 15 winners of its Advanced Proteomic Platforms and Computational Sciences awards totaling $56 over five years. That award is to support development of new tools and technologies for cancer-specific proteomic research.
The third and last component of CPTI is the Clinical Proteomic Reagents Resource, which will serve as a central source for reagents for the research community. Awards and the application process for this will be announced later this year.
CPTI was developed off the promise of the human genome project and the recognition that proteomic methods could be used to detect cancer in its early stages, and possibly help develop cures.
But as Anna Barker, deputy director of NCI, said during a conference call announcing the CPTAC awards, the research community also saw that proteomic research was a swirl of methods and results without many standards.
“One of the issues that became very clear to us early on in our discovery about where [the NCI] should be in proteomics in the next five to 10 years was the revelation that we really don’t have in the proteomics field to this point the opportunity for all investigators to actually work off the same reagents, to work from technologies that are common in the sense that we’re working from standards in terms of technology, that we can reproduce each other’s data from lab to lab, that we can have a high level of confidence that the discovery that we do is actually reproducible from lab to lab,” she said.
“This is an unreliability that we really can’t live in the future with if we want proteomics to become what we all believe that it can be,” added Barker.
It will be the task of the CPTAC award winners to move toward creating some of those standards.
The winners of the CPTAC awards were chosen based on their broad expertise in proteomic research and their familiarity with the use of a wide range of proteomic technologies, the NCI said. The five teams will now work together to evaluate and compare the potential applicability of different commercially available proteomic platforms and analysis software.
The lack of proteomic standards “is an unreliability that we really can’t live in the future with if we want proteomics to become what we all believe that it can be.”
The program teams will focus their research on mass spectrometry and affinity capture platforms. Objectives of the teams include evaluating the performance of proteomic technology platforms and standardizing approaches for developing applications with these platforms; assessing the platforms for their ability to analyze cancer-relevant proteomic changes in human clinical specimens, and developing well-characterized material and bioinformatics resources for the cancer community.
Vanderbilt’s Liebler and his team of about 22 researchers will focus on three things. The first is standardizing the upstream peptide separations. “A lot of this will be an attempt to standardize based on isoelectric focusing of peptides,” building on work done by researchers at RTI International.
The second goal is to improve methods of getting data at the MS/MS level. This will include scanning techniques that Liebler calls data-independent scanning.
“We think that data-dependent scanning, which is sort of the benchmark method for doing tandem MS on ion traps, really introduces much of the variability that you get in shotgun proteomics between replica analyses,” Liebler said.
Finally, his team will be looking to improve downstream bioinformatics tools.
“What this allows us to do is hire people and support people to work on these problems of standardization,” Liebler said. “This program is really designed to hot-rod progress in those key areas of ‘how do we work together,’ ‘how do we improve and standardize our technologies.’”