Background

Background

The Facility is equipped with several very sensitive, high-resolution, mass spectrometers, which allow us to detect, quantify and obtain structural information on extremely small amounts of biological molecules, even in highly complex samples.

This is important because biological samples may only be available in small amounts, and the molecules that take part in the biological processes we study, are often present in cells at very low levels, in complex mixtures of many thousands of different molecules.

Proteins

Much of our work is focused on proteins, the molecules that perform most of the functions of an organism. There are many uses of mass spectrometry in protein biochemistry, but perhaps the most common is in the identification of unknown proteins. It is now possible to identify and quantify several thousand proteins in a single analysis. We use these techniques in three main areas of research:

  1. Characterisation of Protein Complexes.
    The function of most proteins is expressed, not as individual molecules, but as part of multiprotein complexes. A critical first step to understanding these biochemical processes is to identify the proteins that make up the functional complex. We use this approach extensively to study protein complexes involved in many different processes e.g. Tavares et al. (2012).

  2. Post-translational modifications (PTMs).
    Most proteins have their primary structures modified in some way after they are synthesized. There are several hundred known modifications, including phosphorylation, glycosylation, ubiquitination, lipidation, poly-ADP-ribosylation. PTMs can dramatically affect protein activity, interactions, localisation and turnover. Since modification of an amino acid usually results in a change of molecular weight, PTMs can potentially be identified, and their sites of attachment determined, by mass spectrometry. Phosphorylation is of particular interest in signalling as it is the most important mechanism of signal transduction within the cell. Durgan et al. (2021), Odle et al. (2019), Sale et al. (2019).
     
  3. Targeted Analysis.
    Mass spectrometry can be used for the quantitation of known proteins and PTMs, as well as for identification and structural characterisation. Although absolute quantitation is possible, it is more usual to measure changes in the abundance of particular proteins or PTMs under different conditions e.g. increase in phosphorylation of a target site when a kinase is activated. The very high selectivity, sensitivity, dynamic range, and scan speeds of modern mass spectrometers, means that particular proteins or PTMs of interest can be targeted for analysis, even in an extremely complex background, such as a total cell lysate. This allows us to monitor the levels of anything up to several hundred proteins or PTMs in a single analysis, and to see how they change, e.g. following activation of a signalling pathway, or in response to a drug treatment, etc. Tsolakos N, et al. (2018).

DNA

The recent discovery that the TET family of enzymes can oxidise the classical epigenetic mark 5-methyl cytosine to 5-hydroxymethyl-, 5-formyl- and 5-carboxyl-cytosine (hmC, fC, caC) in genomic DNA, generated a great deal of interest in understanding their potential functions.

We developed an ultra-high sensitivity method to analyse these, and some other related modified bases (U, hmU), that allowed us to quantify them in small amounts of genomic DNA. These bases are typically present in extremely low abundance in genomic DNA (<10 - 100 per million bases), which makes their analysis very challenging. Patani et al. (2020), Olova et al. (2018), Booth et al. (2012)