Hi Bethany, please can you tell me about your background and motivation for getting into research?
My background is almost entirely in proteomics and mass spectrometry, with additional focus on bioinformatics. I had the opportunity to work with mass spec during my undergraduate degree at Dundee, and from there I was hooked by the whole thing! I found a PhD in heart proteome dynamics, looking at the protein synthesis and degradation rates within zebrafish hearts to learn about stress. I enjoyed the mass spectrometry parts and got more into the data analysis at that stage with programming using R and Python to make the most of the data.
My first postdoc was in Manchester at the Stoller Biomarker Discovery Centre and the Stem Cell Leukaemia Proteomics Laboratory, where I mostly looked for circulating cancer biomarkers in the blood. We were trying to develop new tests or metrics to stratify patients in addition to their clinical data. One way was using mass spec to assess protein signatures in the peripheral blood of patients going into clinical trials. We could see that you could monitor a certain subset of proteins related to a greater survival rate.
I was first attracted to the role leading the Proteomics Platform for the UK DRI at the University of Dundee, primarily by the scale and variety of work. However, dementia has run in my family for quite a few generations, and so does have a particular personal spot for me, with seeing how it affected my grandmothers. It feels worthwhile to work in this field, even if it's too late to help some of my family members, I can at least try and help other people, and maybe myself in the future.
What is proteomics and when would you use it?
Proteomics is the study of proteins on a large scale - many thousands of proteins – usually using mass spectrometry. Investigations using smaller numbers of proteins or looking at the effects on individual proteins tend to fall out of the proteomics definition, and maybe into cell biology. If you have one single protein of interest, a good selection of antibodies and set-up, then it can be easier to use alternatives to mass spectrometry. But, if you don’t have all these things established and you want fast and accurate results, then I’d recommend mass spectrometry.
There is a lot of opportunity, for instance, you can look at relative levels of a protein of interest compared to all others in your sample, or you can get absolute values and know exactly how much there is. If you want to look at interactors, there are various studies that can be set up to look at what your protein of interest is interacting with, whether it's based on proximity or binding.
What is the UK DRI’s Proteomics Platform?
The Proteomics Platform is a system that allows UK DRI researchers to access mass spectrometry instruments and bioinformatics expertise. Samples are processed either by Douglas Lamont within the FingerPrints facility at Dundee or by myself within the MRC Protein Phosphorylation Unit (PPU) led by Dario Alessi. We've got an enormous range of different techniques available to us, and we want to make these accessible to all the UK DRI, to drive new collaborations. It also allows us to access decades worth of experience in dealing with both study design, bioinformatics, as well as mass spectrometry techniques and even sample preparation techniques. The Platform therefore is designed for not only running samples but also helping with anything ‘proteomics’. Hopefully this internal collaborative platform can save all the groups time, money and energy, opposed to external services.
