image: A photo of the Bruker timsTOF Ultra2
Credit: Bruker
In her lab at the Jackson Laboratory (JAX), Kristen O’Connell wants to know what goes awry in the brains of people with Alzheimer’s disease. One step toward answering this question is comparing the levels of thousands of different proteins in healthy and diseased brain cells to better understand what changes with disease. In the past, carrying out such a comparison, cell by cell, would be nearly impossible. But now, O’Connell has a new tool.
In June, the JAX Protein Sciences Mass Spectrometry Service received a $1.6 million S10 grant from the National Institutes of Health to support the purchase of a new, state-of-the-art mass spectrometry system – the first of its kind of Maine, and one of the first to be installed in the country. The system, called the Bruker timsTOF Ultra 2, allows researchers to analyze the proteins and metabolites contained within individual cells, one at a time, to help advance new diagnostic tools and clinical therapies.
“The level of sensitivity that this equipment has is unprecedented,” said Brian Hoffmann, director of protein sciences and project leader for the grant. “It will allow researchers to get new, very detailed insight into what is happening at the protein level within individual cells that can impact disease.”
Mass spectrometry works by measuring molecules, that are converted into charged ions, within a sample to tell researchers their size and charge – and deduce their identity. For many years, these experiments could only be carried out by analyzing the contents of tens of thousands of cells at once. This would ensure there was enough of any given protein to provide a strong signal. Recently, however, detection systems have begun improving, decreasing the number of cells required in a single sample for accurate detection of proteins and metabolites.
The Bruker timsTOF Ultra2 is one of the first mass spectrometry machines with a high enough sensitivity to analyze proteins and metabolites from single cells. Also supported by the new grant will be a CellenONE X1 accessory instrument for depositing one cell at a time into the well of a plate where it can then be processed and run on the Ultra 2 for analysis. The cell is photographed before being processed, giving researchers additional quality control information on its size (and ensuring that it is just one cell).
“When you use a mix of different cell types from a tissue in mass spectrometry experiments, you don’t really know whether a protein level is different from cell to cell,” said Hoffmann. “Now, we can capture that diversity.”
The new machine, which Hoffmann hopes will be installed and running by late October, helps solidify JAX as a leader in the mass spectrometry space. JAX will be one of the first facilities in North America to have both the Ultra 2 and the Bruker timsTOF FLEX Hoffmann said. Combining the two technologies will give the lab unprecedented detail into both the molecules contained within cells and the locations of those cells within a particular tissue – the basis for single-cell atlases.
All the mass spectrometry systems are available for use by scientists affiliated with JAX, as well as members of the Maine Idea Network of Biomedical Research Excellence (INBRE), a network of 17 educational and research institutions, including Bates, Bowdoin, and Colby colleges and the University of Maine, that share scientific resources to strengthens Maine’s capacity to conduct competitive biomedical research.
“One of the things I really like about working at JAX is that with the Scientific Research Services, we try really hard to push our instrumentation and innovation forward,” said Hoffmann. “Access to this equipment is really valuable for JAX labs and other Maine INBRE labs.”
As for O’Connell, she is already planning to be one of the first in line to use the Ultra 2 equipment. The single-cell nature of the machine means that she can conduct single-cell electrophysiology experiments on neurons from the brain, to study their electrical firing patterns, and then run mass spectrometry on the exact same cells to see how the proteins within each cell impact its electrical activity. By carrying these tests out on both healthy and diseased brain cells, she hopes to gain insight into how molecular changes ultimately cause neurodegeneration -- and how drugs could reverse these changes.
“This instrument will allow us to do for proteins what my lab has already mastered for RNA. Not only will we get a more complete picture of the proteins that regulate cell function, but we will be able to better understand the relationships between RNA and protein and how factors such as age and disease influence the concordance between them – which is not as tight as one might think. This has major implications for understanding disease mechanisms and accelerating the development of effective disease-modifying treatments for Alzheimer’s and other neurological diseases,” said O’Connell.
Hoffmann adds that the single-cell equipment will also be particularly useful for researchers in the JAX Cancer Center looking at cancers and immune cells, where there is known to be high levels of variability between different cells, as well as those tracking small molecule drugs through tissues.