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Bringing Together Next-Generation Proteomics and Next-Generation Sequencing

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Last week saw AB SCIEX and Illumina announce the OneOmics™ project, an exclusive partnership to bring together SWATH™-based next-generation proteomics (NGP) and next-generation sequencing (NGS) tools in a cloud computing environment. 

It is believed that this fast, secure, and streamlined analysis of complex multi-omics data sets, will help advance biomarker discovery and aid research into diseases such as cancer, diabetes, Alzheimer’s, and heart disease.

To learn more about the project and the benefits it provides researchers, we spoke to Mark Cafazzo, MBA, Senior Market Manager, Proteomics  at AB SCIEX 

AB: Can you tell me more about the aims of the OneOmicsTM project?

Mark Cafazzo (MC):We believe that today’s biomarker discovery will lead to tomorrow’s personalized medicine, however there are still challenges to be overcome.

Omics data will be coming in from multiple technologies in multiple formats. The datasets will be large representing a broad range of biological conditions so we need to develop solutions that will allow the comparison and visualization of complex biological results from the multiple omics techniques. To do this we need an integrated workspace where the larger projects can be completed. An environment where data can be processed and compared visualized and shared, in a secure user-friendly workspace:  The OneOmics Data Environment in the cloud.   Bringing the OneOmics project to life.

AB: How did the collaboration with Illumina come about?

MC: Having a technology like SWATH put quantitative proteomics on a larger scale. With the ability to accurately quantify several thousand proteins across hundreds of samples, researchers can now make meaningful biological conclusions.  The next logical step was to integrate those conclusions with other omics results, such as genomics and transcriptomics.  Illumina and AB SCIEX had a single vision and complementary solutions that fit perfectly together.  Both companies also have a large network of internal and external Omics experts who could help bring this vision to reality, quickly.  Not only did we launch our SWATH proteomics applications on BaseSpace; but our partners and collaborators at Advaita, Yale University and the Institute for Systems Biology launched complimentary applications that expand the workflow and represent the first steps in comparing RNA-Seq data and Proteomics data.

AB: We have seen that there are 6 ways SWATH Cloud toolkit will help researchers studying next-gen proteomics, can you tell me a little more about these?

MC: The SWATH Proteomics Cloud Toolkit addresses many customer pain points, from up to 50X faster processing time of large complex data sets  – now done in minutes not days, to ensuring you always have the newest version of your app, and reducing the overhead associated with bioinformatics, IT resources and hardware.  Best of all it allows for collaboration, both across disciplines and the global research community all while helping individual core labs support more institutional labs, faster.  The most significant improvement that harnessing the power of cloud-computing is for the Biologist who can now visualize data in a way that is relevant to them, no more needing special help, you simply use the Protein Expression Browser and go.   

AB: There are currently 4 SWATH Beta Applications on BaseSpace, how would a user register for these?

MC: Users simply go to basespace.illumina.com and sign up for a free account.  Select proteomics from the menu to find the SWATH cloud applications. 

Mark Cafazzo was speaking to Ashley Board, Managing Editor for Technology Networks.