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NIH Funding for Proteomics Fall 3 Percent in FY 2008 as Number of Grants Slides 8 Percent

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This story has been updated from an earlier version.

Funding from the National Institutes of Health for all proteomics-related research shrank by almost 3 percent in fiscal 2008, according to an analysis of NIH data by ProteoMonitor.

For the period covering Oct.1, 2007, to Sept. 30, 2008, NIH funding for proteomics research declined to $125.6 million from $129.1 million in fiscal 2007.

Additionally, the number of grants the agency awarded slid more than 8 percent to 317 in 2008 from 346 in 2007. In many, if not most, cases, funding received in 2008 represented portions of multi-year grants that began in earlier years.

Grants awarded in 2008 averaged $396,072, up 6 percent from an average of $373,029 in 2007, according to the NIH.

Proteomics-directed grants represented about .58 percent of the total 54,644 grants the NIH awarded in 2008, down from .62 percent of the 55,198 it awarded in 2007. In dollar amounts, the grants awarded in 2008 for proteomics represented .59 percent of the total $21.2 billion handed out by NIH during the year. In 2007, proteomics grants made up .61 percent of the $21.3 billion in NIH awards

The analysis was performed on a database of all grants awarded by the agency for fiscal 2008 and was based on grants-title search terms such as “proteomics,” “proteome,” and “mass spectrometer.”

The results are not a comprehensive list of all the grants awarded during the year for proteomics research. For example, experiments based on technology other than mass specs, such as protein arrays, are probably insufficiently captured by the results. Also, on their own, NIH data provide no insight into how many proposals the agency rejected in 2008, or why.

One factor that could play a role in shaping the NIH’s funding priorities in coming years has to do with the Obama administration. The new president said during his campaign that he would double NIH’s budget over the next decade. And some consider Obama’s appointment of Harold Varmus and Eric Lander to co-chair the President’s Council of Advisors on Science and Technology as a boon to research-directed funding.

Varmus, who as director of the NIH under President Bill Clinton from 1993 to 1999 increased NIH funding at a double-digit clip, has fueled hopes that he could influence the Obama White House to loosen NIH’s purse strings.

Meantime, Lander, head of the Whitehead Center of MIT and Harvard, has intimate knowledge of federal funding mechanisms, supports new technology development and basic research, and has been a prolific grant winner in past years.

This week, the US Senate approved an amendment to the Economic Stimulus package that would potentially increase NIH funding for the current fiscal year by $10 billion.

What any of this means to proteomics funding is unclear, but Michael MacCoss, an assistant professor of genome sciences at the University of Washington, said bigger NIH budgets would benefit fields such as proteomics, which some funders continue to regard as high-risk research.

“With more research funding, the pay lines will increase and more high-risk applications will begin to get funded,” MacCoss said in an e-mail to ProteoMonitor. “I think those high-risk applications will be very important to the future of proteomics.”

While federal funding for all science research has been tight in recent years, proteomics researchers have complained that US subsidies for their work have been particularly hard to find, especially in comparison to genomics research.

Indeed, at the JPMorgan Healthcare conference in San Francisco last month, Life Technologies CEO Greg Lucier said that the company’s second-generation sequencing business is better shielded from the general financial turmoil in the private sectors because such platforms have a “funding dynamic semi-removed from the general funding” and still receive “a lot” of government financial support.

In contrast, its mass-spec business has been especially exposed to the collapse of the broader equity markets, Lucier said. And in a recent report, Wall Street analyst firm Leerink Swann said that large capital-equipment firms, such as mass-spec manufacturers, will likely miss out on any immediate benefit from increased NIH funding in coming years [See PM 01/08/09].

At the annual conference of the Human Proteome Organization in the summer, apparent resistance to funding proteomics projects, particularly large-scale ones, was on full display during a session with various funding agencies throughout North America and Europe, including NIH. During a session to discuss HUPO’s proposed $1 billion, 10-year Human Proteome Project, funders repeatedly alluded to an image of proteomics as a field that has failed to deliver in the clinical setting, which has made the discipline a hard sell [See PM 08/21/08].

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While getting funding is especially hard for young scientists without a track record or the experience to sell their work to the NIH, even those who have been in the field for decades say getting money for proteomics research is a challenge that has been getting tougher.

“There isn’t much interest per se in [funding] proteomics” projects, Fred Regnier, a professor of analytical chemistry at Purdue University, told ProteoMonitor this week.

The problem is simple, he said: There simply isn’t enough money in NIH’s pot for everyone. As a reviewer for NIH, he said that the number of proposals in recent years has skyrocketed while funding for NIH has generally remained flat or declined.

In addition, he said, the agency has had trouble getting enough reviewers, and in some fields, including proteomics, the reviewers are not familiar with the intricacies and issues of the field. The result is that some grant proposals may have been turned down not on their merits, but because reviewers may not be able to properly judge them.

The key to a successful NIH proposal, he said, is “coupling proteomics with disease” in order to try to answer some biological question. “Show a disease relationship, [and proteomics is] going to enhance a cure,” he said.

But even while shaping a proposal toward a clinical application may help it get funded, Regnier and others also said that NIH needs to show greater willingness to support basic and fundamental research, which may not lead to immediate benefits in the clinic.

“The key to the future of proteomics might lie in a technology that hasn’t been conceived of yet,” MacCoss said, adding that proposals “that I believe were my most innovative frequently fared the worst,” in the application process. “We could miss this without funding specifically allocated to basic research where the application is not yet clearly defined.”

Where'd the Money Go?

Though funding was down in 2008, it did not fall in line with any particular recent trend in NIH funding for proteomics. In fact, over the past few years, the funding trend has been erratic.

For instance, the $129.1 million that NIH handed out in 346 proteomics-related grants in 2007 was 26 percent above the $102.4 million in 282 grants doled out in 2006. But compared to 2005, when NIH funding for proteomics-related funding totaled $131 million, 2006 declined 22 percent in dollar figures [See PM 12/14/06].

In 2008, the NIH funded 274 research teams at 147 universities, hospitals, institutions, and companies covering all proteomics-research applications, including pure research, technology development, equipment purchases, and training.

The single-largest grant, $2.7 million, was awarded to Steven Carr’s team at the Massachusetts Institute of Technology for a project titled “Measuring cancer biomarker candidates by targeted MS and Ab enrichment.” [For a list of the 20 grants which received the most funding, see here]

At the other end of the spectrum, Eric Cooper at the University of Rochester received the smallest grant, $24,398, to study the regulation and proteomics of polyubiquitin signaling.

While the majority of researchers who received funding did so for only one project, some received NIH grants for multiple proeomics projects. For example, Richard Smith at Battelle Pacific Northwest National Laboratories received grants for six different projects totaling $5.8 million. Regnier, meanwhile, received four grants amounting to $1.5 million, and John Yates at the Scripps Research Institute was awarded $1.4 million covering four projects.

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Similarly, a handful of institutions were especially well-represented in the NIH pie. Six researchers at the University of California, Los Angeles, split eight grants, the same as at Yale University. And six researchers split seven NIH awards each at the University of Colorado, Denver; MIT; and the University of Michigan.

But proteomics researchers looking to maximize their chances at getting NIH funding may want to head to the University of Washington: 11 research teams there split 12 NIH grants.

Researchers there said that that is not a coincidence and several factors may account for the phenomena, including a long history of proteomics research at the school, which may have given it a head start over other institutions and helped its researchers applying for mass spec-based proteomics. Both Yates and Ruedi Aebersold, who now teaches at the Federal Technical University in Zurich and at the University of Zurich, both in Switzerland, were on staff at UW at one time.

“The effects of these pioneers are still being felt at UW today, approximately nine years after their departure,” MacCoss said.

The school, he added, has aggressively recruited faculty across different disciplines and departments who both develop and apply proteomics tools and technologies.

“Unlike other institutions where resources are often used to support the development of a core, at UW, efforts have been focused on recruiting faculty who are expected and want to support their own research programs from federal grants,” he said. “This approach has been very successful because proteomics at UW has more that paid for itself and an even greater body of scientists have had their research supported, not through a core per se, but as part of a collaboration.”

Lynn Schnapp, an associate professor of medicine at UW specializing in pulmonary and critical care medicine at the school, received $155,332 in NIH funding in 2008 for a project called “Proteomic-based approach to ventilator associated pneumonia.” The school’s success at securing funding for proteomics research is reflective of its overall success at getting NIH funding, she said.

The school has formal programs, including those to teach young researchers “survival skills” at the start of their careers, to introduce them to how the NIH works and how to apply for NIH grants, she said. In addition, formal and informal mentorship increase the chances of a researcher’s grant proposal passing the grade at the NIH.

“Compared to other institutions, I’d say we’re a more collaborative environment and don’t eat our young as much as some other places might,” she said.

The school’s proximity to other prominent institutions in the area, such as the Institute for Systems Biology and the Fred Hutchinson Cancer Center, as well as companies such as Insilicos, LabKey, and Rosetta Biosoftware, have also helped to create a “collaborative environment [that] enables biologists to interact with mass spec folks [to] come up with good proposals,” Schnapp said.

While the majority of NIH grants awarded in 2008 went to US-based entities, three were awarded to researchers based elsewhere. Marianne Sadar, at the British Columbia Cancer Agency, received $209,928 for a grant titled “Genomic and proteomic analysis of prostate cancer,” and Stephen Dorus at the University of Bath, UK, received two grants totaling $50,428 to characterize the human and mouse sperm proteomes.

Not surprisingly, many of the grants awarded last year were for clinically directed research, including numerous awards for biomarker research, as well as grants for research into cancer, neurodegenerative diseases, and heart disease.

Some grants were also for work in less-traditional subject areas. For instance, the NIH last year awarded Christine Wu from the University of Colorado, Denver, $234,065 for a project entitled, “Proteomic dissection of withdrawal-induced excessive drinking.” Also last year, Melinda Lull of Pennsylvania State University received $26,545 for her work entitled, “Proteomic adaptations of abstinence-induced behavioral sensitization to cocaine.”

The list of those receiving funds in 2008 contained some of the most recognized names in proteomics, including Mike Snyder at Yale who received $586,499 split into two grants, each titled, “Training in genomics and proteomics technologies.” Sam Hanash at the Fred Hutchinson Cancer Center received $458,633 for his project titled, “Proteomics biomarkers development laboratory,” and his colleague at the Hutch, Martin McIntosh, received a total of $834,449 in two separate grants for his project looking into breast and ovarian cancer using affinity-based serum proteomics.

Also, Donald Hunt at the University of Virginia received two grants for research using mass spectrometry totaling $1.6 million.

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