Press Release

AB SCIEX and Illumina Collaborate to Create World’s First Multi-omics Cloud-Computing Environment

Integration of SWATH™ Apps with BaseSpace® Brings Next-Generation Proteomics and Next-Generation Sequencing Together for the First Time

Framingham, MA and San Diego, CA – October 2, 2014 - AB SCIEX and Illumina (NASDAQ: ILMN) announced today 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.

The AB SCIEX SWATH™ Proteomics Cloud Tool Kit suite of applications will be hosted in BaseSpace, Illumina’s applications store and cloud-based informatics community dedicated to advancing genomic analysis. This partnership enables BaseSpace as a single location for genomics and proteomics "big data." With fast, secure, and streamlined analysis of complex multi-omics data sets, this solution will help advance biomarker discovery and aid research into diseases such as cancer, diabetes, Alzheimer’s, and heart disease.

"The integration of proteomic and genomic data analysis through a partnership with

AB SCIEX and Illumina is an exciting collaboration that will bring democratization of computational efforts, general access and standardization of data analysis, and provide a platform for systems biology in life sciences," said Leroy Hood, President of the Institute for System Biology.

The patented AB SCIEX SWATH™ Proteomics software solves the "missing data problem" wherein traditional "shotgun" proteomics measures an incomplete set of proteins that are difficult to reproduce. SWATH™ makes reproducible proteome research feasible for the first time across many samples and is further enhanced through integration with Illumina NGS technologies.

"SWATH™ software is a patented innovation that allows thousands of proteins to be examined at once with almost no method development, and now with our cloud-based applications customers can process data 50 times faster," said Rainer Blair, President of AB SCIEX. "The OneOmics project will enable better outcomes in omics research. We have developed four SWATH apps to support processing, analyzing, and visualization of proteomics mass spec data to extract biological insights."

As NGP and NGS generate ever-increasing volumes of data, this partnership addresses a bottleneck in biomedical research by helping to securely store, retrieve, and manage large-scale, complex data sets, and visualize them in a biological context. Ruedi Aebersold, Ph.D., professor at the Institute of Molecular Biology at the ETH in Zurich, comments, "Using this platform, researchers will be able to make predictable, actionable, and testable models of disease more quickly and efficiently. In essence it moves the focus of multilevel analysis of biological systems from wet-lab data acquisition into the computational domain, where large data sets can be shared globally".

The AB SCIEX SWATH™ Cloud Toolkit brings a growing list of BaseSpace apps to extract biological insight from SWATH™ proteomics mass spectrometry data, including:

  • Protein Expression Extractor – for processing raw mass spectrometry data
  • Protein Expression Assembler – for protein fold-change analysis
  • Protein Expression Browser – to visualize results in biological context
  • Protein Expression Analytics – for data quality review

"These new proteomics tools add systems biology capabilities to BaseSpace, creating an easy-to-use, cloud-based environment that enables rapid data analysis for a growing range of applications," said Nicholas Naclerio, Senior Vice President, Corporate Development and General Manager, Enterprise Informatics for Illumina. "Now, BaseSpace is making informatics accessible to anyone searching for a truly interdisciplinary, systems-level understanding of biology."

Informatics solutions available in BaseSpace Apps allow customers to utilize tools from a growing community of academic, commercial, and open source providers. The AB SCIEX SWATH™ Proteomics Cloud Toolkit is available in BaseSpace at


AB SCIEX helps to improve the world we live in by enabling scientists and laboratory analysts to find answers to the complex analytical challenges they face. The company's global leadership and world-class service and support in the liquid chromatography-mass spectrometry industry have made it a trusted partner to thousands of the scientists and lab analysts worldwide who are focused on basic research, drug discovery and development, food and environmental testing, forensics and clinical research. With over 25 years of proven innovation, AB SCIEX excels by listening to and understanding the ever-evolving needs of its customers to develop reliable, sensitive and intuitive solutions that continue to redefine what is achievable in routine and complex analysis. For more information, please go to

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AB Sciex Instruments Are For Research Use Only. Not for use in diagnostic procedures.

The trademarks mentioned herein are the property of AB Sciex Pte. Ltd., Illumina, Inc., or their respective owners, as the case may be. AB SCIEX™ is being used under license. © 2014 AB SCIEX.

About Illumina

Illumina is transforming human health as the global leader in sequencing and array-based technologies. The company serves customers in a broad range of markets, enabling the universal adoption of genomic solutions in research and clinical settings. To learn how Illumina is unlocking the power of the genome, visit and follow @illumina.

Illumina Forward-Looking Statements

This release may contain forward looking statements that involve risks and uncertainties. Important factors that could cause actual results to differ materially from those in any forward-looking statements are detailed in our filings with the Securities and Exchange Commission, including our most recent filings on Forms 10-K and 10-Q, or in information disclosed in public conference calls, the date and time of which are released beforehand. We do not intend to update any forward-looking statements after the date of this release.

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