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Advanced Protein Centre of The Hospital for Sick Children Adopts Genedata Expressionist for Mass Spectrometry

Mass Spectrometry facility uses Genedata Expressionist for label-free quantitation of raw data files in the identification of trace cancer biomarkers—solution will be shown at HUPO 2010

September 20, 2010
Sydney, Australia

Genedata, a leading provider of advanced software solutions for drug discovery and life science research, today announced the Mass Spectrometry Facility of the Advanced Protein Centre at the Hospital for Sick Children (Toronto) is using Genedata Expressionist®. The system is an enterprise solution for Mass Spectrometry (MS)-based biomarker discovery, data processing, and sophisticated statistical analysis. Capable of handling large-volume data sets, it features an annotation framework, and advanced spectrum and chromatogram visualizers. Genedata will demonstrate Genedata Expressionist at the HUPO 9th Annual World Conference (September 19–23; Booth 52).

“A large part of our business is cancer biomarker identification and we want to offer label-free proteomics to our research community,” said Paul Taylor, manager of the Advanced Protein Centre. “We methodically researched all available options from vendor-specific to Open Source solutions and none compared to Genedata Expressionist’s analytic and visualization capabilities for MS. Most other solutions are for small machines and make far too many compromises, eliminating lots of data on first-pass filtering. Being able to quantify very small signals allows us to dig deeper into the proteome, which expands the potential biomarker list. Genedata Expressionist doesn’t filter out data. It analyzes all the data, easily handling tens to hundreds of 300- to 400- megabytes raw data files. Bottom line—Genedata got the math right. The underlying algorithms work in Genedata Expressionist to give us automated label-free quantitation.”

Eye-opening Visualization
While the Advanced Protein Centre is using Genedata Expressionist, including the new Refiner MS module for label-free quantitation, the system also addresses a range of set-ups from simple one-dimensional spectra to complex experiments involving labeled technologies in proteomics, metabolomics, and lipidomics. Genedata Expressionist features direct search engine integration from within workflows for interactive searches with Mascot (used by the Advanced Protein Center), ChemSpider, and HMDB, as well as offline import results from Mascot, SEQUEST, and MetaboCard - without information loss. Combining novel visualization for real-time interactive data quality assessment, Refiner MS uses sophisticated algorithms for intensity and alignment correction, peak detection, quantification, and matching.

“Genedata Expressionist visualization is literally eye-opening when looking at data,” continued Taylor. “For example, the 3D plots tell you so much more than the histograms we are accustomed to using and the viewer creates a mega-picture of what is going on. The viewer alone has enabled better quality control, allowing us to modify and improve our methods files. We’re using the Genedata solution to review data with our researchers and other proteomics facilities—it’s fast and intuitive and works as a great stand-alone solution.”

“Label-free proteomic experiments are not easy to analyze and the Advanced Protein Centre is successfully stretching the boundaries in biomarker research,” noted Dr. Othmar Pfannes, CEO of Genedata. “We’re delighted that Genedata Expressionist is contributing to this innovative work.  Moreover, the Centre’s adoption of the Genedata Expressionist system validates how Genedata solutions integrate advanced algorithms that align with and support our customer’s specific business processes and workflows.”

About Genedata

Genedata transforms data into intelligence with innovative software solutions that incorporate extensive biopharma R&D domain knowledge. Multinational biopharmaceutical organizations and cutting-edge biotechs around the globe rely on Genedata to digitalize and automate data-rich and complex R&D processes. From early discovery all the way to the clinic, Genedata solutions help maximize the ROI in R&D expenditure. Founded in 1997, Genedata is headquartered in Basel, Switzerland with additional offices in Boston, London, Munich, San Francisco, Singapore, and Tokyo.
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Allison Kurz
Public Relations


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Being able to quantify very small signals allows us to dig deeper into the proteome, which expands the potential biomarker list

Paul Taylor
Manager, Advanced Protein Centre