Applied Biosystems/MDS Analytical Technologies Advance Proteomics Research Through Suite of Integrated Mass Spectrometry Solutions

New Software and Reagents Expand Productivity and Efficiency for Targeted Quantitative Proteomics FOSTER CITY, Calif.–Applied Biosystems (NYSE:ABI – News), an Applera Corporation business, and its joint-venture partner, MDS Analytical Technologies, a business unit of MDS Inc. (NYSE:MDZ – News) (TSX:MDS – News), today announced the availability of a suite of integrated mass spectrometry-based solutions for conducting targeted quantitative proteomics studies. Designed for Applied Biosystems/MDS Analytical Technologies’ industry-leading triple quadrupole and hybrid triple quadrupole/linear ion trap mass spectrometry systems, these solutions include software packages and consumables that enable scientists to more effectively quantify proteins in biomarker research or cell biology. These new tools address the needs of scientists in industry and academia who are seeking to quantify many specific proteins and peptides in complex biological samples. Thousands of proteins may be present in any specific laboratory sample; however, scientists are often most eager to study the subset of those that are typically lower in abundance and are changing in response to a disease. Targeted mass spectrometry is emerging as a powerful tool for these quantitative assays, yet key challenges remain. The need for higher order multiplexing, improved reproducibility and more rapid assay development for these protein panels is critical for scientists to continue to drive forward their biomarker initiatives in a streamlined, efficient manner. Applied Biosystems/MDS Analytical Technologies’ targeted quantitative proteomics solutions are uniquely positioned to address these challenges because they are designed to deliver consistency along with simplified, one-touch accessibility to world-class technology across the entire workflow. These new tools include: mTRAQ™ reagents are chemical labeling kits for use in targeted proteomics experiments using MRM analysis that can be used to create global internal standards to provide an internal reference for every protein, peptide and post-translational modifications in a sample, in a simple one-hour step. Based on proprietary Applied Biosystems technology, mTRAQ reagents are designed to improve analytical reproducibility for quantitative experiments without the need for costly custom synthetic peptides. Scheduled Multiple Reaction Monitoring is a feature that focuses instrument cycle scans for specific analytes based on the timeframe that those analytes will be entering the instrument. In proteomics, this means the instrument can scan up to 10 times more peptides with better analytical precision and yielding more information about each one. The Scheduled MRM™ Algorithm is part of Applied Biosystems/MDS Analytical Technologies’ updated operating system, Analyst® 1.5 Software, which powers its mass spectrometry systems. MRMPilot™ Software is a new software program for use with Applied Biosystems/MDS Analytical Technologies QTRAP® Systems that enable rapid development of robust MRM assays for peptides and proteins utilizing data acquired during discovery experiments. MRMPilot Software automatically builds MRM assays and utilizes the unique MIDAS™ Workflow of the QTRAP system for more seamless and far more efficient transition from discovery to validation. These assays complement existing widely used antibody-based assays, while requiring up to ten-fold less time to develop and eliminating the need for purified proteins. MultiQuant™ Software is a new software package for use with Applied Biosystems/MDS Analytical Technologies mass spectrometers that processes MRM data for quantitative information. The software enables the efficient processing of many analytes and samples at the same time, with an emphasis on the requirements for processing protein/peptide quantitative workflows. New Approach to Mapping Proteomes at the Institute of Molecular Systems Biology An example of research enabled by these new tools is being performed by Dr. Bruno Domon, a research scientist at the Institute of Molecular Systems Biology in Zurich, Switzerland. Dr. Domon’s laboratory has developed a workflow to perform proteomics assays that was previously thought impossible due to constraints in the number of peptides that could be measured by the mass spectrometer in a targeted approach. His team is applying this workflow to biomarker studies on samples in several disease areas with an emphasis in cancer and diabetes. An initial step is to compile a set of putative biomarkers from genomics or proteomics studies or published research, and then to create Scheduled MRM Algorithm-based assays to quantitate the proteins, thus bridging the span from discovery to validation. His work has been enabled by early access to mTRAQ reagents in combination with a 4000 QTRAP LC/MS/MS system. The QTRAP System is a premier hybrid triple quadrupole/linear ion trap mass spectrometer that delivers quantitative and qualitative data within a single experiment. Dr. Domon’s team attempts to map entire proteomes. Beyond a simple cataloging of the proteins present in a sample, they seek to measure and understand multiple forms of each protein and what the changes that occur in the levels of these proteins may signify. They have already completed the yeast proteome and are currently working on others including drosophila. In both their biomarker and mapping studies, the Scheduled MRM Algorithm-based workflow has allowed them to measure proteins at much lower levels than could be done with their previous approach, providing the ability to scan a catalog of several hundred proteins in the course of an hour. “Our laboratory has proposed a full paradigm shift in how proteomics mass spectrometry experiments are done, from a ‘shotgun’ approach that was very effective in the early days of proteomics, to a targeted, hypothesis-driven approach,” said Dr. Domon. “Proteome studies are incredibly complex. This method opens new opportunities to get deeper into proteomes and get more comprehensive data sets, and it enables us to potentially complete in a few days what would normally require several months.” Improved Understanding of Virus Propagation at Yale University Dr. Colangelo is also working with Drs. Megan Shaw and Peter Palese at Mount Sinai School of Medicine as part of the Northeast Biodefense Center to study how influenza virus interacts with the host cell machinery during the viral life cycle. Their research has shown that numerous host cell proteins are incorporated into the virus particle along with the virus-encoded proteins. He has used MRMPilot and Scheduled MRM to quantitate all nine influenza virus proteins and 32 host proteins found within the virus particle in a single experiment. In one 75-minute experiment using sMRM, he was able to generate results that originally took approximately 8 hours to perform. “For our virus studies, our collaborators want to know the precise concentration of each of these host proteins, because if we begin to understand the role that these host proteins play in the virus life cycle, it may create new opportunities for the design of anti-influenza virus therapies to halt virus replication,” said Dr. Colangelo. “For both the biomarker and virus studies, the scheduled MRM workflow allows us to generate much more information in each experiment, with much lower costs, and improved sensitivity.” Applied Biosystems is a global leader in the development and commercialization of instrument systems, software, consumables and services for the life-science market. Through a joint venture with MDS Analytical Technologies, the company is a leader in providing complete workflows for the mass spectrometry market, based on industry-leading platforms, software and new application workflows. For more information about Applied Biosystems/MDS Analytical Technologies proteomics solutions, please visit teomics/index.htm (Due to its length, this URL may need to be copied/pasted into your Internet browser’s address field. Remove the extra space if one exists.) About Applera Corporation and Applied Biosystems Applera Corporation consists of two operating groups. Applied Biosystems serves the life science industry and research community by developing and marketing instrument-based systems, consumables, software, and services. Customers use these tools to analyze nucleic acids (DNA and RNA), small molecules, and proteins to make scientific discoveries and develop new pharmaceuticals. Applied Biosystems’ products also serve the needs of some markets outside of life science research, which we refer to as “applied markets,” such as the fields of: human identity testing (forensic and paternity testing); biosecurity, which refers to products needed in response to the threat of biological terrorism and other malicious, accidental, and natural biological dangers; and quality and safety testing, such as testing required for food and pharmaceutical manufacturing. Applied Biosystems is headquartered in Foster City, CA, and reported sales of approximately $2.1 billion during fiscal 2007. The Celera Group is a diagnostics business delivering personalized disease management through a combination of products and services incorporating proprietary discoveries. Berkeley HeartLab, a subsidiary of Celera, offers services to predict cardiovascular disease risk and optimize patient management. Celera also commercializes a wide range of molecular diagnostic products through its strategic alliance with Abbott and has licensed other relevant diagnostic technologies developed to provide personalized disease management in cancer and liver diseases. Information about Applera Corporation, including reports and other information filed by the company with the Securities and Exchange Commission, is available at, or by telephoning 800.762.6923. Information about Applied Biosystems is available at All information in this press release is as of the date of the release, and Applera does not undertake any duty to update this information unless required by law. About MDS Analytical Technologies MDS Analytical Technologies is a newly established MDS Inc. business unit and is a world-class organization comprised of two main lines of business. The Sciex product portfolio offers proven market leadership in mass spectrometry through its joint ventures with two of the world’s leading analytical instrumentation and life sciences companies, Applied Biosystems, a business of Applera Corporation, and PerkinElmer Inc. Molecular Devices’ product portfolio is the gold standard in high-performance bioanalytical measurement systems that accelerate and improve drug discovery and other life sciences research. Find out more at or Applied Biosystems Forward Looking Statements Certain statements in this press release are forward-looking. These may be identified by the use of forward-looking words or phrases such as “should,” “expect,” and “planned,” among others. These forward-looking statements are based on Applera Corporation’s current expectations. The Private Securities Litigation Reform Act of 1995 provides a “safe harbor” for such forward-looking statements. In order to comply with the terms of the safe harbor, Applera Corporation notes that a variety of factors could cause actual results and experience to differ materially from the anticipated results or other expectations expressed in such forward-looking statements. These factors include but are not limited to: (1) rapidly changing technology and dependence on the development and customer acceptance of new products; (2) sales dependent on customers’ spending policies; and (3) other factors that might be described from time to time in Applera Corporation’s filings with the Securities and Exchange Commission. All information in this press release is as of the date of the release, and Applera does not undertake any duty to update this information, including any forward-looking statements, unless required by law. © 2008 Applera Corporation and MDS Inc. All rights reserved. For research use only. Not for use in diagnostic procedures. Applera, Applied Biosystems, iTRAQ and AB (Design) are registered trademarks and mTRAQ is a trademark of Applera Corporation or its subsidiaries in the US and/or certain other countries. Analyst is a registered trademark and MultiQuant and MRMPilot are trademarks of Applied Biosystems/MDS Analytical Technologies Instruments, a joint venture between Applera Corporation and MDS Inc.

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