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A P4 partnership
March 2013
by Lloyd Dunlap  |  Email the author


FRAMINGHAM, Mass.—Seattle- based Institute for Systems Biology (ISB) and AB SCIEX have signed a multiyear agreement to collaborate on the development of methods and technology in proteomics mass spectrometry (MS), with the goal of redefining biomarker research and complementing genomics through comprehensive quantitative proteomics analysis.  
The partnership aims to advance the development of a new vision for medical care, which ISB expects to become more personalized and better able to help prevent the onset of diseases in the future, thanks to research into "P4 medicine" underway at the institute, and now supported by its new collaboration with AB SCIEX.  
ISB's concept of P4 medicine—described as predictive, preventive, personalized and participatory—requires a combination of analytical tools, workflows, databases, collaborations and computational strategies.  
"Quantifying enormous numbers of protein analytes at the same time is a critical need to accelerate P4 medicine and the democratization of proteomics, a revolution that is akin to the sequencing of the genome and the democratization of DNA," observes National Medal of Science award winner Dr. Leroy Hood, president and co-founder of the ISB.  
Hood adds that "AB SCIEX's SWATH is a game-changing technique that essentially acts as a protein microarray and is the most reproducible way to generate comprehensive quantitation of the entire proteome."  
SWATH acquisition is a data-independent acquisition mass spectrometry workflow that can quantify virtually all detectable peptides and proteins in a complex sample—all in a single analysis. In doing so, it generates a digital record of the entire proteome from biobank or tissue samples that can be mined retrospectively for years to come.  
Aaron Hudson, senior director of academic and omics business at AB SCIEX, explains what SWATH technology—what he says is a new generation of proteomics analytics—brings to the game.  
"Shotgun proteomics was a mainstay for a long time for identification 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 the other hand, targeted proteomics, which can quantitate with great accuracy, takes "a lot of method development," Hudson notes, which again, limits its utility in the broader biological world.  
Enter SWATH, which combines the best of both worlds, Hudson states, and provides reproducible results "again and again." Also, it produces a complete set of MS data without any method development, opening the technique to broad adoption by more biologists.  
Committed to an open policy of sharing data and methods, ISB will make the SWATH libraries available to the global scientific community to accelerate the use of SWATH for other biological research. Utilizing the depth in proteomics technology development and underpinned by the extensive proteomics computational resources in data interpretation tools, standards initiatives and database development under the leadership of Dr. Robert Moritz, the ISB will develop new SWATH technologies and tools to enable the community to quickly adopt comprehensive quantitative proteome analysis.  
"Having the proteomics data standardized across laboratories and across samples really enables us to quantitate entire proteomes at a level that hasn't been done before," Moritz states. "We aim to define markers that can predict whether a patient will respond to a certain treatment or not, and applying SWATH will play a big part in taking our advancements to another level. Not only can we now complement the breadth of genomics, but we will also have the much-needed libraries and software development going forward to make data-sharing easier and standardized."
Code: E031312



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