The Institute for Systems Biology and the scientific tools company AB Sciex have entered into a multi-year agreement to collaborate with the aim of improving biomarker research by making it easier for researchers to conduct experiments, and share and retrieve results. Together, the two partners hope to do for proteomics what the sequencing of the human genome has done for the field of genomics.

The technology, dubbed SWATH, will allow researchers to quantify enormous numbers of proteins simultaneously. SWATH will be able to work with a wide variety of samples without requiring standardized preparation and can quantify virtually all detectable peptides and proteins in a complex sample, the partners say.

“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 Leroy Hood, president and co-founder of the Institute for Systems Biology. “It generates a digital record of the entire proteome that can be mined retrospectively for years to come.”

Proteomics, an area of research that identifies not only which proteins are in a sample, but also how many of them are there and how their interactions and modifications change across disease states and environmental conditions, can be used to track disease. Information and biomarkers discovered and validated through proteomics research helps identify patients at risk for disease, facilitates prevention and early detection, enables screening of drug efficacy, and allows monitoring disease progression and response to treatment.

The collaboration combines advances in AB Sciex’s tools and technology to analyze the chemical structure of proteins with the institute’s expertise of systems biology—an area of multidisciplinary research that explores the genetic, molecular, and cellular networks that drive disease.

Together, they hope advance the field of personalized medicine in the hopes of improving healthcare, reducing its cost, and creating new opportunities to transform its practice by ultimately shifting the focus from treating disease to preventing them.

One of the biggest potential benefits of the collaboration is that it will create proteomics datasets that can be compared against clinical samples. By so doing, the partners hope to redefine biomarker research and provide comprehensive proteomics information to investigators. The resulting data from the project will be freely available to the global scientific community.

AB Sciex’s technology generates a digital archive of all possible particles in a single sample for permanent storage. That will allow researchers in the future to access the analysis without additional patient samples. Because the technology can analyze proteins or cell components without special prior treatments, researchers across the globe can use the same system and same analytic tools, enabling large scale comparisons.

Rob Moritz, proteomics research director for the Institute of Systems Biology says having the proteomics data standardized across laboratories and across samples will enable research to quantify entire proteomes at a level that hasn’t been done before. “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,” he says. “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.”