This story originally ran on March 2.
By Tony Fong
At least $356.5 million was handed out in grants for proteomics research by the National Institutes of Health in fiscal 2009, including nearly $55 million in stimulus funding, according to an analysis of an NIH database.
The funding covers the period between Oct. 1, 2008, and Sept. 30, 2009. In total, 1,026 proteomics grants were awarded for FY 2009, averaging $347,468 per grant.
For the life sciences, the past year represented a funding jackpot of sorts, and for proteomics, it was no different. After several years of essentially flat or shrinking budgets at NIH, funding to the agency grew 3.2 percent in FY 2009 to $30.4 billion, from $29.5 billion in FY 2008.
More importantly, the agency received an additional $10 billion stemming from the American Recovery and Reinvestment Act, or stimulus bill, covering FY 2009 and 2010. Last year that resulted in at least 154 stimulus-related grants for proteomics research totaling $54.9 million, an average of $356,394 per grant.
The total number of grants and dollar amounts directed to proteomics was calculated based on an analysis of NIH's RePORTER database using keywords such as "proteomics," "proteome," "mass spectrometer," and "protein biomarkers."
The results are not a comprehensive list of all NIH grants that were awarded for proteomics research during the past year, and some grants may not have been captured by the keyword terms. In some instances, some grants were captured by the keyword search but excluded from the final list because it was unclear from the project's abstract whether proteomics was a focus of the research.
It is also unclear how many of the 1,026 grants were new grants and how many were awards for existing grants originally approved in earlier years.
Regardless, the results provide a snapshot of what the NIH funding environment was like for proteomics last year and what kinds of projects are attracting the attention of the agency.
While a wide range of research was supported by the grants, two categories of funding accounted for a disproportionate share of the funding last year: One-third of the NIH grants for proteomics either supported proteomics facilities or funded biomarker-based research.
Based on a keyword search of grant titles, proposals for proteomics centers received 171 grants in FY 2009, making that category the best-funded in terms of the number of awards given out. The grants totaled $45,589,573 for an average of $266,606 per grant.
Trailing behind were grants to biomarker-directed projects, with 168 grants, though the actual number of grants for projects that include a substantial biomarker component is almost certainly higher because not all of them had "biomarker" in the title or abstract.
The 168 grants totaled $58,292,757, an average of $346,981 per grant.
Among the recipients of such awards was Steven Carr at the Broad Institute who was given two grants totaling $3,233,760 for a project directed at measuring candidate cancer biomarkers by targeted mass spectrometry and antibody enrichment. One grant was for $2,833,858, the single largest grant for biomarker research.
Also, Lee Hood at the Institute for Systems Biology received an $892,482 grant to purchase a Thermo Fisher Scientific LTQ Orbitrap XL to create proteome maps. And Sam Hanash at the Fred Hutchinson Cancer Research Center received a $443,657 grant to continue research into identifying tumor antigens that "induce a humoral response" in cancer patients, according to the grant abstract.
Not So Stimulating
Despite the approval of the stimulus funds last year, the major mass spec vendors said throughout 2009 that they had seen little or no benefits of such funding to their business. This was reflected in the NIH data, which showed that just 22 grants — of which nine were ARRA grants — totaling $11,732,979 were handed out for the acquisition of a mass spec platform.
Thermo Fisher was the main beneficiary of both stimulus and non-stimulus grants for mass spec acquisitions, supporting claims made by company CEO Marc Casper that half of all stimulus funds tied to mass specs went to the firm — 12 grants were specifically for the purchase of the company's instruments.
Two grants were for an AB Sciex platform, and Agilent, Bruker, and Waters instruments were each named once among the grants. The remaining five mass spec grants did not identify the instruments being purchased.
Of the stimulus funds for platform acquisitions, five were for a Thermo Fisher instrument, one each for a Waters and Agilent instrument, and two were for platforms from unidentified vendors.
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In addition to grants for the purchase of new systems, one grant for $4,673 was awarded for an upgrade to an existing system. The grant was awarded to Peter O'Connor at Boston University in order to continue development of data systems to allow two Fourier transform mass specs "to be highly flexible and completely independent of one another," according to the grant's abstract.
Two grants were provided for education and training on mass specs.
Eleven grants were awarded for the development of new mass spec technologies totaling $1,353,529 for an average of $135,353 per grant. These included a $41,494 award to Andrew Krutchinsky, formerly at Rockefeller University and now at the University of California, San Francisco, who is using it to develop a tandem mass spec that will increase "the efficiency of linked-scan analyses by [more than] 100-fold over conventional linked-scan instruments," according to the grant's abstract.
Alexander Misharin from Science and Engineering Services received a $99,999 award to build a novel hybrid ion mobility-FT-IRC platform. If successful, the instrument could extend the range of capabilities of conventional FT-IRC platforms and establish "novel ways of utilizing the powerful FT-ICR instrumentation in the fields of glycomics and elucidation of the protein conformation and structure," according to the abstract.
And Marvin Vestal of Virgin Instruments received a $100,000 grant to develop a new MALDI-TOF platform that can compete with FT-ICR and Orbitrap instruments on resolving power and mass accuracy but have greater speed, throughput, sensitivity, and dynamic range than is currently possible with electrospray technology.
At the MSACL conference in San Diego held earlier this month, Vestal presented on his work developing the platform [See PM 02/12/10]
Projects aimed at developing mass spec-based methods and strategies received $4,588,204 spread among 10 grants. Catherine Costello at Boston University Medical Campus received two grants, one for $2,344 for research directed at identifying hemoglobin variants and post-translational modifications, and one for $11,836 to continue development of a method coupling thin layer chromatography with vibrationally cooled MALDI-FTMS
Mike MacCoss at the University of Washington received $27,708 — one of 13 grants totaling $489,741 — in funding to developing a method based on field asymmetric ion mobility spectrometry "as a fast gas-phase separation technique interfaced with a bench-top ion trap mass spectrometer for increasing the peak capacity of proteomics analyses without losses in speed or revenue," according to the grant's abstract.
Funding for array-based proteomics lagged far behind mass spec-based proteomics when it came to NIH funding last year. In all, 24 projects using protein arrays received $8,292,570. The University of California, Los Angeles' Aydogan Ozcan received the largest grant, $2,310,000, "to create the next generation of microarray technologies to achieve an unprecedented mega-throughput," he said in his grant abstract. Specifically, he said, "label-free imaging of millions of DNA/protein microspots would be feasible per second."
In addition, Joshua LaBaer of Arizona State University received $100,000 for work on nucleic acid programmable protein arrays, or NAPPA, he developed. In continuing research he aims to adapt the technology for the "rapid and efficient" screening of sera from cancer patients for antibodies to 1,000 known and potential tumor antigens in multiplex for the early detection of breast cancer.
"Using tests sets and validation sets of serum samples derived from patients with early-stage breast cancer, we will determine the frequency, sensitivity and specificity of autoantibodies to tumor antigens for the early diagnosis of breast cancer," LaBaer said in the grant's abstract.
The 1,026 proteomics-related grants awarded in FY 2009 were divided among at least 625 different sets of principal investigators. Two awards did not list PIs.
Among those who were listed as PIs in multiple projects is John Yates, currently at the Scripps Research Institute. Projects on which he was listed as the PI received $775,181 split among 19 grants. Mark Chance at Case Western Reserve University received 10 grants for $2,056,923, while Boston University's Costello received 18 grants totaling $3,241,706.
Richard Smith at Pacific Northwest National Laboratories received $13,765,583 divided among 16 grants.
Rolf Apweiler at the European Molecular Biology Laboratory received the biggest NIH grant last year for proteomics research, $4,999,953 to support UniProt. Specifically, the grant is to, among other things, develop the UniProt Knowlegebase, further develop the UniProt Archive, and create the UniProtKB entry history server "to ensure comprehensive coverage of all protein sequences and their annotation history," according to the grant abstract.
Larry Arthur at Science Applications International Corp. received the next highest amount, $4,517,214 related to a restructuring that the Laboratory of Proteomics and Analytical Technologies at the National Cancer Institute-Frederick is undergoing.
For a list of the top-10 proteomics grants awarded in 2009 based on amount, click here.