Product News: In the Forefront of Research into Protein Folding and Macromolecular Complex Assembly - University of Leeds Publishes Results Acquired With Waters SYNAPT High Definition MS System

04 Dec 2007

Waters Corporation announced today that the University of Leeds' Astbury Centre for Structural Molecular Biology has published the results of protein research conducted with its newly-acquired Waters® SYNAPT High Definition MS™ (HDMS) System in the Journal of the American Society of Mass Spectrometry (JASMS).

The SYNAPT® HDMS System is being used by the Ashcroft Laboratory to study the function of biological molecules. In an article appearing in the December 2007 issue of the JASMS, researchers at Leeds describe the successful separation and analysis of various folded forms of the proteins cytochrome c and beta-2-microglobulin, an achievement the Ashcroft Laboratory hopes will lead to a more complete understanding of the biological processes responsible for amyloid fibril formation, bacterial pilus aggregation and virus capsid assembly – all associated with debilitating diseases.

Proteins are carefully folded, three-dimensional long-chain molecules assembled by the human body. When properly folded they regulate normal bodily functions. Several high profile diseases, including Alzheimer’s, Creuzfeldt-Jakob’s, and Parkinson’s, can develop when certain proteins normally folded into a particular shape become misfolded, causing a chain of events that can lead to self-aggregation and amyloid fibril formation. Dr. Alison Ashcroft and her colleague Prof. Sheena Radford at the University of Leeds are studying one such protein, beta-2-microglobulin, to try to understand how it forms such fibrils which accumulate in the joints of dialysis patients and which are associated with dialysis-related amyloidosis. A detailed understanding of these processes at the molecular level will aid in the design of therapeutics.

New Form of Mass Spectrometry Giving New Dimensions to Biological Research
As a tool, conventional mass spectrometry is an excellent method for differentiating between proteins having different masses. However, as different conformers, or folded forms, of a particular protein have identical masses, it is virtually impossible to differentiate them by conventional means. That’s where the Waters SYNAPT HDMS System, and its embedded ion mobility technology, has helped the University of Leeds.

“A protein can fold into a very compact 3-D structure or under certain conditions it can unfold into a more expanded structure. Even though these different 3-D structures have the same mass and mass-to-charge (m/z) ratio, the ion mobility capability of the SYNAPT HDMS System can separate them and tell you how much of the protein is in its folded form vs. the unfolded form. And as the cross-sectional areas of the two protein conformers are different, by being able to separate them by shape, the SYNAPT HDMS System allows us to distinguish between the various protein forms. The results are really amazing,” says Dr. Alison Ashcroft, Reader in Biomolecular Mass Spectrometry and Mass Spectrometry Facility Manager.

The SYNAPT System from Waters has provided the lab with new insights into the assembly process. “It’s adding a new dimension to our research. We can now quantify the amount of protein that is in its native state and the amount that is unfolded and partially folded. We can also monitor which particular conformers are consumed during the assembly process. This is providing important new insights and detail into how biomolecules work at the molecular level,” adds Dr. Ashcroft.

Waters introduced the SYNAPT HDMS System at the American Society of Mass Spectrometry annual meeting in Seattle in June of 2006. It is the first commercially-available mass spectrometer with the ability to analyze ions by their size, shape and charge in addition to mass.

A Strategy for Managing Terabytes of Scientific Data
Given its complement of five different types of mass spectrometers, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Wellcome Trust, managing data is a huge challenge for The Ashcroft Laboratory. To manage data files more efficiently, the laboratory has chosen Waters NuGenesis Scientific Data Management System (SDMS).

“Backing up data daily to DVD’s was getting out of hand. The SDMS takes data once a day from five mass spectrometers and backs it up automatically and our post-graduate students and post-docs can look at the data directly from their office computers. It’s important we archive data because the government funding bodies request we store data for five or 10 years from the date it was created. Graduate students take four years to get their Ph.D., so they need the data accessible for four years or more, especially if they are writing papers after getting their Ph.D.,” comments Ashcroft.

“People that aren’t analytical chemists tend to think of a mass spectrometer as a sophisticated weighing machine. Often they don’t realize that you can look at a protein’s functionality and behaviour with the instrument and they can be quite surprised when they find out,” says Ashcroft.

The full reference for Dr. Ashcroft’s article in the Journal of the American Society of Mass Spectrometry is:
Monitoring co-populated conformational states during protein folding events using ESI-IMS-MS, D. P. Smith, K. Giles, R. H. Bateman, S. E. Radford, A. E Ashcroft, J. Am. Soc. Mass Spectrom., 2007 Dec; 18 (12): 2180 – 90, DOI:10.1016/j.jasms.2007.09.017

Reprint requests should be addressed to A. E. Ashcroft, Astbury Centre for Structural Molecular Biology, Astbury Building, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT UK or email: