Waters Introduces New Capabilities for Proteomic Research

Waters Corporation is announcing a new version of its ProteinLynx™ Global SERVER software, including enhancements to Waters® Protein Expression System, at the annual meeting of the Association of Biomolecular Resource Facilities (ABRF), February 11 - 14.

Waters® ProteinLynx Global SERVER™ (PLGS) 2.2.5 software features new tools which will allow researchers to identify and quantify proteins and biomarkers more efficiently.

Waters Protein Expression System featuring PLGS was the first commercial product for cost-effective and practical quantitative proteomics without the use of isotope labelling technologies. PLGS 2.2.5 extends this breakthrough technology with improved algorithms for efficient protein quantification and identification across large patient/sample sets or time-course studies.

A new quantification module in PLGS allows quantitative data to be generated at the protein or peptide level using any of the commercially available or user-defined labeling technologies such as SILAC™, AQUA™, ICAT®, iTRAQ™, etc. The ability to perform both ’label free’ and ‘isotopic labeling’ approaches now means that PLGS provides unparalleled flexibility to analyze proteomics samples of varying type and complexity.

PLGS 2.2.5 provides a ‘step change’ in the ability to identify proteins efficiently in complex samples by incorporating a new algorithm which enables identification of proteins from MSE data (E - elevated collision energy) acquired from a Q-Tof type mass spectrometer. In an LC/MS experiment a proprietary and patented ‘parallel’ peptide fragmentation protocol is employed to provide a 100% duty cycle on all detectable peptides in a protein digest. This new approach results in significantly higher sequence coverage and confidence in protein identification than traditional ‘Data Dependent Acquisition’ (DDA) MS/MS methods.

Other enhancements for PLGS 2.2.5 include new data visualization tools that visually depict what happens to the protein concentration over a large number of samples or conditions. These new tools are especially important for researchers performing time-scale studies during which changes in the protein profile are carefully monitored at intervals, e.g. drug time course studies.

Finally, for researchers publishing their scientific findings in peer-reviewed scientific journals, PLGS 2.2.5 will have access to a number of popular formats including peaklist, eXtensible Markup Language (XML), and the mzData Format as required by the Human Protein Organization (HUPO) Proteomics Standards Initiative for Mass Spectrometry.

These and other enhancements being introduced at ABRF 2006 will be discussed in Booth #311 and in several posters during the scientific session which will be available after the conference at www.waters.com/posters.