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Despite Sequester, NIH Funding for Proteomics Up Slightly in FY 2013

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NIH grants for proteomics research were up slightly in 2013, according to an analysis by ProteoMonitor, with roughly $134 million handed out during the US government's fiscal 2013, a 2.5 percent increase over $130 million in 2012.

The funding covers the period between Oct. 1, 2012, and Sept. 30, 2013. In total, 320 grants were awarded for FY 2013, averaging $419,000 per grant.

The numbers indicate that NIH funding for proteomics has remained relatively stable even as the federal sequester cut the agency's 2013 budget by $1.71 billion, or roughly 5 percent, suggesting that the field has outperformed the general life sciences space in terms of winning federal funds.

ProteoMonitor calculated the number of grants and dollars awarded for proteomics research via a search of NIH's RePORTER database using keywords including "proteome," "protein biomarker," "protein array," and "mass spectrometer." The results of this search were then manually curated to eliminate grants that contained one or more keywords in the description but that were not, in fact, for proteomics research.

Given that some awards may not have been captured by the keyword search, the results are not necessarily a comprehensive list of 2013 NIH grants for proteomics. Nonetheless, they offer a glimpse as to how the field fared in the year's reduced funding environment as well as a look at the sort of projects and instrumentation that attracted agency awards.

Prominent among those receiving funds were researchers associated with the second phase of the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium. Launched in August of 2011, CPTAC 2 aims to combine protein biomarker discovery and verification studies in tumor tissue samples with genomic characterizations of those same samples done by The Cancer Genome Atlas project.

The project has established research centers at eight institutions including Washington University in St. Louis, the University of North Carolina, Boise State University, Pacific Northwest National Laboratory, the Broad Institute, Fred Hutchinson Cancer Research Center, Johns Hopkins University, and Vanderbilt University, which it plans to fund to the tune of $75 million to $120 million over the effort's five-year lifetime.

Several CPTAC researchers were among NIH grant recipients in 2013. For instance, Vanderbilt University researcher Daniel Liebler received $2.6 million for a proteome characterization center under the CPTAC project. Liebler also received a separate $584,000 grant from NIH to fund a biomarker development laboratory as part of the NCI's Early Detection Research Network.

Wash U researcher Matthew Ellis likewise won NIH funds for CPTAC work, securing $2.1 million to develop cancer proteome centers at Wash U and the University of North Carolina.

Broad Institute researcher Steven Carr received $3 million for his lab's work within the CPTAC effort, specifically multiple-reaction monitoring and SISCAPA-based analyses of the proteomes and phosphoproteomes of glioblastoma, breast, ovarian, and kidney cancer samples.

A number of significant grants were also awarded for work on developing protein affinity reagents. Johns Hopkins researcher Jef Boeke, for instance, received $1.8 million for the development of monoclonal antibodies against human transcription factors; Andrew Bradbury at Los Alamos National Laboratory won $1.3 million for work on a high-throughput platform for selecting renewable recombinant polyclonal antibodies; Arizona State University Biodesign Institute researcher John Chaput received $1.3 million for development of bivalent synthetic antibodies to the human proteome; and Brian Kay at the University of Illinois received $1.1 million for work on recombinant affinity reagents.

In terms of mass spec instrumentation, Thermo Fisher Scientific's Orbitrap Elite and AB Sciex's TripleTOF 5600 were among the most popular models in 2013, with six grants totaling $3.9 million going to purchase Orbitrap Elite instruments and three grants totaling $1.6 million going toward TripleTOF 5600 machines. Thermo Fisher's Q Exactive was also relatively popular, scoring two grants worth a total of $1.1 million.

In all, nine grants totaling $5.3 million went towards the purchase of Thermo Fisher instruments, with an award for a TSQ Vantage triple quadrupole joining the grants for the six Elites and two Q Exactives. There were four grants for AB Sciex instruments totaling $2.2 million. These included the three TripleTOF awards along with an award for a 5500 QTRAP.

One award, a $165,328 grant to Susan Weintraub at the University of Texas Health Science Center, San Antonio, went towards purchase of an Agilent instrument, a 6225 ESI-TOF. Weintraub also received a $190,080 grant to support the center's mass spec shared resource.

In total, $7.7 million in grants went towards the purchase of mass spec instrumentation in 2013. This was up 7 percent from $7.2 million in 2012. As in 2013, Thermo Fisher led the way in 2012, with four grants for its Orbitrap Velos instrument, totaling $2.6 million. 2012 also saw two grants for AB Sciex 5500 QTRAP machines; one grant for a Bruker Solarix FT-ICR instrument; one grant for an Agilent 6230AA TOF; one grant for a DVS Sciences CyTOF instrument; and two grants for triple quadrupoles instruments for which no make was specified.

A number of 2013 awards also supported mass spec technology and method development. University of Wisconsin-Madison researcher Josh Coon received $222,619 to develop a gas chromatography system to be interfaced with a Thermo Fisher Orbitrap instrument. The University of Washington's Michael MacCoss won a $372,731 award to further develop his lab's Skyline software tool for targeted mass spec-based proteomics.

University of Washington researcher James Bruce received $294,110 for an effort to increase mass spec throughput by developing mass spec arrays for use on ion cyclotron resonance instruments. The technology, he said in the grant's abstract, could increase MS/MS acquisition speeds by an order of magnitude.

Oregon State University's Douglas Barofsky was granted $339,977 for work on developing a single tandem mass spec dissociation cell capable of performing collision-induced dissociation, infrared multiphoton dissociation, electron capture dissociation, electron detachment dissociation, electron transfer dissociation, and electron impact excitation of ions from organics, individually or in combination.

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