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Feb 6, 2013

Cutting a SWATH through Personalized Medicine

  • The Institute for Systems Biology (ISB) signed a multi-year agreement with AB Sciex to collaborate on the development of methods and technology in proteomics mass spectrometry with the goal of redefining biomarker research and complement genomics through quantitative proteomics analysis. The aim is to help advance the development of a new approach to medical care.

    Led by ISB president and co-founder Leroy Hood, M.D., Ph.D., ISB’s research is being accelerated by SWATH™ Acquisition, a data-independent acquisition (DIA) mass spectrometry workflow that reportedly can quantify virtually all detectable peptides and proteins in a sample from a single analysis. ISB will be using the AB Sciex TripleTOF® 5600+ System and an Eksigent ekspert™ nano-LC 400 System as the instrument platforms on which to conduct the protein identification and quantitation. The TripleTOF 5600+ System can reportedly provide the high speed necessary for SWATH Acquisition. ISB also plans to use SelexION™ technology, a recent advancement in differential ion mobility, in the future to advance its research.

    “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,” says Dr. Hood, “It generates a digital record of the entire proteome that can be mined retrospectively for years to come.”

    ISB shall support the development of SWATH libraries similar to its SRMAtlas project for the human proteome, pioneered by Rob Moritz, Ph.D., and his collaborators, and the proteomes of other clinically relevant organisms. “With complete proteome-wide libraries, ISB provides the basis to support comprehensive SWATH analysis,” said Dr. Moritz, who is ISB's proteomics research director.

    ISB aims to make the SWATH libraries available to the global scientific community to accelerate the use of SWATH for other biological research. ISB will develop new SWATH technologies and tools to enable the community to 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,” said Dr. Moritz. “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 have the much-needed libraries and software development going forward to make data-sharing quite easier and standardized.”

    AB Sciex forged this alliance with ISB through the AB Sciex Academic Partnership Program to help broaden the availability of new technologies to researchers delving into OMICS research around the world.

    “What ISB does with SWATH will set a new benchmark in proteomics research,” said Rainer Blair, president of AB Sciex. “Our collaboration with ISB will help drive SWATH into the mainstream of analytical science and make comprehensive, reproducible and simplified omics data more accessible to biologists around the world.”

    SWATH Acquisition was first made available to the worldwide scientific community back in April through a collaboration between AB Sciex and ETH Zurich.


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