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A P4 partnership

The Institute for Systems Biology and AB SCIEX partner to make medical care more ‘predictive, preventive, personalized and participatory’

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Written byLloyd Dunlap

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Lloyd Dunlap
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Published In

Volume 9 - Issue 3 | March 2013

March 2013

FRAMINGHAM, Mass.—Seattle-based Institute for SystemsBiology (ISB) and AB SCIEX have signed a multiyear agreement to collaborate onthe development of methods and technology in proteomics mass spectrometry (MS),with the goal of redefining biomarker research and complementing genomicsthrough comprehensive quantitative proteomics analysis.

The partnership aims to advance the development of a newvision for medical care, which ISB expects to become more personalized andbetter able to help prevent the onset of diseases in the future, thanks toresearch into "P4 medicine" underway at the institute, and now supported by itsnew collaboration with AB SCIEX.

ISB's concept of P4 medicine—described as predictive,preventive, personalized and participatory—requires a combination of analyticaltools, workflows, databases, collaborations and computational strategies.

"Quantifying enormous numbers of protein analytes at thesame time is a critical need to accelerate P4 medicine and the democratizationof proteomics, a revolution that is akin to the sequencing of the genome andthe democratization of DNA," observes National Medal of Science award winnerDr. Leroy Hood, president and co-founder of the ISB.

Hood adds that "AB SCIEX's SWATH is a game-changingtechnique that essentially acts as a protein microarray and is the mostreproducible way to generate comprehensive quantitation of the entireproteome."

SWATH acquisition is a data-independent acquisition massspectrometry workflow that can quantify virtually all detectable peptides andproteins in a complex sample—all in a single analysis. In doing so, itgenerates a digital record of the entire proteome from biobank or tissuesamples that can be mined retrospectively for years to come.

Aaron Hudson, senior director of academic and omics businessat AB SCIEX, explains what SWATH technology—what he says is a new generation ofproteomics analytics—brings to the game.

"Shotgun proteomics was a mainstay for a long time foridentification and quantitation," he says. But the process relies on"information-dependent acquisition," he adds.

In the hands of MS experts, it has been a trusted method,but for the broader biological world, reproducibility can be an issue. On theother hand, targeted proteomics, which can quantitate with great accuracy,takes "a lot of method development," Hudson notes, which again, limits itsutility in the broader biological world.

Enter SWATH, which combines the best of both worlds, Hudsonstates, and provides reproducible results "again and again." Also, it producesa complete set of MS data without any method development, opening the techniqueto broad adoption by more biologists.

Committed to an open policy of sharing data and methods, ISBwill make the SWATH libraries available to the global scientific community toaccelerate the use of SWATH for other biological research. Utilizing the depthin proteomics technology development and underpinned by the extensiveproteomics computational resources in data interpretation tools, standardsinitiatives and database development under the leadership of Dr. Robert Moritz,the ISB will develop new SWATH technologies and tools to enable the communityto quickly adopt comprehensive quantitative proteome analysis.

"Having the proteomics data standardized across laboratoriesand across samples really enables us to quantitate entire proteomes at a levelthat hasn't been done before," Moritz states. "We aim to define markers thatcan predict whether a patient will respond to a certain treatment or not, andapplying SWATH will play a big part in taking our advancements to anotherlevel. Not only can we now complement the breadth of genomics, but we will alsohave the much-needed libraries and software development going forward to makedata-sharing easier and standardized."

A P4 partnership

About the Author

Lloyd Dunlap

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Published In

March 2013

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