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Thermo Fisher Scientific Updates Proteomics Analysis Software

Published: Wednesday, September 12, 2012
Last Updated: Wednesday, September 12, 2012
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Protein Metrics’ Byonic Search Software adds “ultimate search strategy” to Proteome Discoverer software version 2.0 to streamline post translational modification analysis.

Thermo Fisher Scientific Inc. introduced Thermo Scientific Proteome Discoverer software version 2.0 for analyzing qualitative and quantitative proteomics data. As part of the release, the company announced a non-exclusive agreement with Protein Metrics, Inc. to license the company’s Byonic™ database search software, adding next-generation capability to streamline analysis of glycopeptides and other post translational modification data.

The company is featuring Proteome Discoverer software and a range of other proteomics solutions within booth 707 during the HUPO 11th Annual World Congress in Boston from Sept. 9 - 13.
Thermo Fisher will also feature the Proteome Discoverer software at HUPO during a lunchtime workshop on the latest findings in glycomics and glycoproteomics. The workshop runs from 12:00 - 1:30 p.m. on Tuesday, Sept. 11.  Chris Becker, Protein Metrics CEO, will also discuss the software during a presentation at IMSC in Kyoto on September 19. The presentation,Automated Identification of Intact Glycopeptides from Complex Samples,is co-authored by scientists from Protein Metrics, Thermo Fisher and Institute of Biological Chemistry, Academia Sinica in Taipei, Taiwan.

“We call this the ‘product-dependent acquisition’ because users are able to acquire data from only the molecules of interest such as glycopeptides,” said Andreas Huhmer, marketing director, Thermo Fisher. “This greatly simplifies glycoprotein analysis and makes it accessible to a much wider range of scientists. Glycoproteomics workflows are no longer as complex as many people believe.”

“We are delighted to be working with Thermo Fisher to integrate our Byonic software into Proteome Discoverer software,” added Becker. ”As the capabilities of Thermo Fisher’s mass spectrometer systems reach new heights, it is important that the software keep pace to bring the most extensive and accurate information to users.”

Proteome Discoverer software version 2.0 combines spectral library searching with classical database searching for fast, highly reliable identification of true positive peptide spectrum matches. Huhmer calls this “the ultimate search strategy.” The software also includes a multi-threaded SEQUEST® search engine that takes advantage of the latest computer architecture to accelerate database searches. The software’s peptide and protein false discovery rate and probability (PFDRP) feature provides high-confidence identification of proteins and peptides. High-confidence measurement of phosphorylation sites is provided by PhosphoRS 2.0, included in Proteome Discoverer 2.0.

The new version of Proteome Discoverer software also generates reports automatically, saving users large amounts of time and effort. This is especially useful for large studies where hundreds of files are interpreted.

Proteome Discoverer software version 2.0 is compatible with all current Thermo Scientific Orbitrap-based LC/MS instruments. Planned shipping date is December 1, 2012.

Protein Metrics’ PreviewTM software is also now available through Thermo Fisher. Preview software samples MS/MS data to measure mass errors, digestion specificity and modifications for subsequent full protein database search.

In addition to Proteome Discoverer, Thermo Fisher is featuring a wide range of other qualitative and quantitative proteomics solutions within booth 707. These include:

•    The Thermo Scientific Q Exactive hybrid quadrupole Orbitrap® mass spectrometer, designed for confident identification, quantification and confirmation in a single run
•    Thermo Scientific SimGlycan software, designed to speed the characterization of complex glycans through automated interpretation of MS data
•    Thermo Scientific Mass Spectrometry Immunoaffinity pipette tips, which enhance protein detection and reduce sample preparation
•    Thermo Scientific NanoDrop UV-Vis Spectrophotometers, which facilitate concentration measurements of 2 mL protein samples without cuvettes, capillaries or dilution

SEQUEST® is a registered trademark of the University of Washington.


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