Thermo Fisher Scientific and Proteome Sciences Form Protein Biomarker Collaboration

The collaboration unites the talent and resources of the proteomics reagent team at the Thermo Fisher Scientific Biomarker Research Initiatives in Mass Spectrometry (BRIMS) Center with Proteome Sciences (PS) to further develop quantitative proteomic workflows that are based on best-in-class reagents and hardware and software for biomarker discovery and validation.

Proteome Sciences has installed Thermo Scientific LTQ Orbitrap Velos and TSQ Vantage mass spectrometer systems at its research laboratories in Frankfurt, Germany to extend its biomarker discovery and validation workflows. As part of the collaboration, Proteome Sciences will combine state-of-the-art Thermo Scientific mass spectrometry technology with its integrated PS Biomarker Services workflow that is powered by tandem mass tag (TMT™) reagents.

“The Thermo Scientific Orbitrap LTQ Velos mass spectrometer, with its unique combination of HCD and ETD fragmentation, will allow us to extend the scope of proteomic services we offer to customers,” said Ian Pike Ph.D., COO of Proteome Sciences. “When using the TSQ™ Vantage high-sensitivity triple quadrupole mass spectrometer in combination with our proprietary TMT tandem mass tag technology for assay development, we can offer the most integrated biomarker discovery, qualification and assay validation workflows in the industry. We have already successfully used TMT technology to develop mass spec assays for blood biomarkers in Alzheimer’s disease and are extending our coverage for other proprietary biomarkers in cancer and brain damage. Access to these resources is available through our PS Biomarker Services Division*.”

Development of Tandem Mass Tag Reagents

Proteome Sciences and Thermo Fisher Scientific have already been working together following the licensing of Proteome Science’s isobaric mass tagging reagents. The companies have recently expanded the range of products through the launch of a cysteine-reactive sixplex TMT® set and an anti-TMT® antibody used to enrich labelled peptides that improve sensitivity and breadth of coverage for many low-abundance proteins. Proteome Sciences holds patents covering the field of isobaric mass tagging, and further products will be launched in 2011 based on the core TMT chemistry.

John Rogers Ph.D., manager of Thermo Scientific Pierce Proteomics Reagents R&D, said: “We have been aggressively pushing the capabilities of the TMT technology to take full advantage of the outstanding mass spec performance of the core tag structure. The introduction of cysTMT™ reagents and an immobilized antibody to the TMT reagent core structure is just the start of the process, and further TMT products with additional reactive selectivity are in the pipeline. One major development scheduled for 2011 is a sixplex set that can be used in both HCD and ETD fragmentation modes on the LTQ Orbitrap Velos mass spectrometer. Clearly, TMT technology leads the field in isobaric mass tagging and, by using the same core chemistry across the TMT range, quantitative mass spec studies for biomarker discovery and targeted quantification can readily be performed without changing mass spec set-up.”

Clinical Research Applications of Mass Spectrometry

Over the past three years, Proteome Sciences has been working with team members at the BRIMS Center to adapt workflows for isotope dilution mass spectrometry assays based on the technique of selected reaction monitoring (SRM). With the installation of the highly sensitive TSQ Vantage triple quadrupole mass spectrometer and Thermo Scientific Accela LC system at its Frankfurt labs, Proteome Sciences will expand its relationship with BRIMS to develop its proprietary biomarker assays in Alzheimer’s disease and cancer to develop these for clinical research applications.

Although SRM-based methods are widely used for clinical measurement of small molecules, these methods are only now becoming practical in the routine measurement of more complex biological agents such as proteins,” said Ian Jardine, Ph.D., vice president global R&D at Thermo Fisher Scientific. “Through collaboration, our two companies can provide the best-in-class hardware, software and reagents that can potentially lead to the use of this powerful technology into clinical applications.”

Dr. Malcolm Ward, CTO of Proteome Science’s UK development group, commented: “The interaction with the staff at BRIMS has provided us with early access to the data analysis software needed for the scheduling and interpretation of multiplex quantitative protein assays. This has culminated in our developing standard workflows to streamline assay set-up that are now incorporated into Thermo Scientific Pinpoint software.”

“The ability to use the different forms of TMT technology in discovery and then for biomarker candidate verification is extremely powerful,” commented Dr. Pike. “More TMT reaction chemistries will widen the scope of our biomarker research and, in combination with the ongoing developments in Thermo Scientific mass spectrometer platforms, will bring even the relatively low-abundant proteins within reach of MS assays.”

For more information about Thermo Scientific solutions, please visit the Thermo Scientific booths 55, 56, 65 and 66 during HUPO 2010. For more information about Thermo Scientific solutions for proteomic research, please call +1 800-532-4742, email [email protected] or visit www.thermoscientific.com/ms.

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*Additional Information: Developing Protein Biomarker Assays as a Service

In 2008, Proteome Sciences started the move toward routinely using SRM assays for biomarker candidate identification. Whereas immunoassays are slow and expensive to develop and have to be done one marker at a time, SRM methods have the advantage of being both rapid and relatively inexpensive to set up. Many proteins can be measured in a single test. Proteome Sciences has set up the PS Biomarker Services Division to provide a seamless workflow where isobaric TMT reagents are used to increase performance in discovery and then isotopic TMT reagents are used to rapidly set up SRM assays for candidate biomarker identification. This is supported by the Proteotype DB database of more than 4,500 human and 1,500 rodent proteins that Proteome Sciences has identified by mass spectrometry during its 10 years of internal research and development.

Proteome Science contact details

Media contact information: Adrian Shaw by telephone on +44 1483 271291 or by email [email protected]

Company contact information: Ian Pike Ph.D. by telephone on +44 1932 865065, email [email protected] or visit www.proteomics.com