Thermo Fisher Scientific Bolsters Proteome Dynamics Offering with HUPO Product Launches

Thermo Fisher Scientific Inc., the world leader in serving science, will introduce a new proteomics workflow solution at HUPO 2008, plus major upgrades to two premier Thermo Scientific software packages. Complementing the recent launch of the Proteome Discoverer software platform, which provides a comprehensive and expandable platform for quantitative and qualitative proteomics data, these latest additions provide further enhancements of the Thermo Scientific Proteome Dynamics offering.

Proteome Dynamics is an integrated portfolio of proteomics solutions, including reagents, sample preparation kits and protocols, mass spectrometers and application-specific bio-software designed to work together to facilitate the identification, quantitation and characterization of proteins. The new introductions include:

• Automated Phosphopeptide Workflow – a complete, protocol for the automated analysis of phosphopeptides
• SIEVE™ 1.2 – a major upgrade to the label-free differential analysis software used to measure and identify changes in proteins and peptides based on the comparison of LC/MS datasets
• ProSightPC™ 2.0 – which extends the capabilities of the industry-leading top-down identification software to now support the identification and characterization of proteins from all high mass accuracy tandem mass spectrometry experiments.

Over the past decade, the field of proteomics has progressed to the point that it has a significant impact on cutting edge developments in biology and medicine. Thermo Fisher has been moving science forward with the development of powerful proteomics research that breaks the boundaries of traditional qualitative proteomic analyses to advance quantitative proteomics, thereby creating a dynamic picture of proteomes.

The new Automated Phosphopeptide Workflow combines the power of Thermo Scientific technologies with the Pierce® Phosphopeptide Enrichment Kit, the Kingfisher® Flex magnetic bead purification system and the LTQ Orbitrap™ XL ETD hybrid mass spectrometer to enable fully automated analysis of phosphopeptides. Scientists involved in mapping signalling pathways have found that phosphopeptide enrichment by immobilized metal and metal oxide affinity chromatography followed by MS analysis is a powerful technique. However, the complexity of the samples and low-throughput handling procedures have proved a major handicap. The new Thermo Scientific integrated protocol provides a simple, robust solution to these problems. “The output from each step in the sample preparation and analysis process is optimized,” explains Andreas Huhmer, director of proteomics marketing at Thermo Fisher Scientific. “The workflow enables scientists to move seamlessly through the whole protocol.”

Also launching at HUPO 2008 will be Thermo Scientific’s SIEVE 1.2 Software. SIEVE automates the label-free differential expression of proteins and peptides by comparing LC/MS datasets of “healthy” or control samples to treated or “diseased” samples to determine if there are differences – all without the need for isotopic labels. Previously, only pairs of single analyses or datasets could be compared. However, in research areas such as biomarker discovery, being able to look at trends in the data is essential, and SIEVE 1.2 now provides the ability to look at multiple time points or dosing points within a single trend analysis.

“The primary requests we received from customers after the first release of SIEVE was the ability to monitor how their proteins were changing over time and to make it easier to interpret the statistical results on both a peptide and protein level,” says Amy Zumwalt, proteomics marketing programs manager at Thermo Fisher Scientific. “To address this need we added the trend analysis feature for this version and also completely re-engineered the user interface. The new wizard- driven interface makes it easy to set up differential experiments and interpret statistical results.”

Also being showcased for the first time will be Thermo Scientific ProSightPC 2.0 software, initially designed to facilitate top-down identification and characterization of proteins and now enhanced to support all high mass accuracy, high resolution MS/MS proteomics experiments.. ProSightPC 2.0 enables high-throughput processing of all accurate mass MS2 data, whether from top-down, middle-down or bottom-up experiments, and includes the characterization of proteins with known PTMs. “Thermo Scientific ProSightPC 2.0 is specifically geared towards hybrid spectrometry techniques and also supports data generated by the new LTQ Orbitrap XL ETD mass spectrometer,” says Andreas Huhmer. “This provides researchers with a unique tool to decipher intricate differences of protein isoforms and variants.”

Like SIEVE, a new graphical interface has made it much easier to use. And, importantly, it now offers automatic LC-MS file processing. Previously, peaks had to be chosen manually before processing, but now an entire chromatogram can be chosen, allowing all the peaks to be analyzed automatically.