Proteomics @ Liverpool

An internal website for the Protein Function Group and Collaborators


About me
My enthusiasm for animals is what led me to my degree in Bioveterinary Science, during which I completed an honours project, within PFG, investigating methods to isolate and characterise the isoforms of skeletal muscle parvalbumin in carp (Cyprinus carpio) using proteomic techniques. I continued working on this project over a summer studentship and was then offered a Ph.D. as part of the InterCEPT grant, working in collaboration with Prof. Rob Beynon (Liverpool), Prof. Simon Gaskell (Manchester) and Dr Kathryn Lilley (Cambridge).

My Ph.D. project investigated strategies to determine rates of protein turnover within both a prokaryotic and more complex whole animal model using metabolic stable isotope labelling (dynamic-SILAC). Protein turnover in E.coli was assessed using an ‘unlabelling’ trajectory, following the loss of [13C6]arginine from proteins using 1D SDS-PAGE with MALDI-ToF and also LC-MSE with a Synapt G1. In the whole animal model I investigated protein dynamics in mouse tissues from animals fed a semi-synthetic diet containing 50% [2H8]valine. Non-invasive sampling methods were used wherever possible to reduce the number of animals required. This was possible because of the high concentration of major urinary proteins (MUPs) present in the urine. As MUPs are synthesised in the liver they provide an opportunity to study temporal changes in this tissue via urine sampling.

My first post-doctoral research position involved absolute quantification of the translational machinery of yeast (Saccharomyces cerevisiae), using both label-free mass spectrometry and label-mediated QconCAT strategies. QconCATs are recombinant genes, expressed heterologously in E.coli, encoding concatenations of proteotypic peptides unique to proteins of interest. This information was then used to parameterise mathematical models of protein synthesis to investigate key points in the pathway.

An additional project that I was involved in during this time investigated the proteomics of seminal vesicle and sperm proteins in the house mouse (Mus musculus domesticus). By feeding a stable isotope labelled diet to male mice it was possible to track the baseline replacement rates of proteins from seminal vesicles and the caudal epididymis in a non-competitive environment. This initial work supported a successful grant application to further study the proteomic changes during sperm competition in rodent models, which is now the focus my current research project.
During my current post-doctoral project a variety of MS techniques, including both label-free and stable isotope label-mediated strategies, will be employed for the identification and quantification of proteins present in seminal vesicles of mice exposed to different levels of sperm competition. Another interesting aspect of the project hopes to determine the overall investment of individual males (in terms of sperm/seminal vesicle proteins) to mating, depending on the sperm competition experienced. Initial experiments will focus on the house mouse (Mus musculus domesticus) but we hope to also study sperm competition in the bank vole (Clethrionomys glareolus) as this is a more promiscuous species, often experiencing high levels of competition during mating.

I have gained substantial experience using MALDI-ToF MS on both a Waters Micro and Shimadzu Axima-ToF2 instrument. I am also a confident user of the LTQ ion trap and LTQ-Orbitrap Velos mass spectrometers (Thermo Electron) for both MS and MSMS data acquisition and as such I have some responsibilities for general assessment and maintenance of these instruments and associated UPLC systems (U300, Dionex and Nano-Acquity, Waters). I also have experience with the Synapt-G1 and G2 mass spectrometers (Waters) using MSE data-independent acquisition for label-free quantification of complex biological samples and the Xevo triple-quadruple (Waters) for more targeted analysis.


  • Amy Claydon, Andrea Pennington, Steven Ramm, Jane Hurst, Paula Stockley and Robert Beynon (2012). ‘Heterogenous turnover of sperm and seminal vesicle proteins in the mouse revealed by dynamic metabolic labelling’. Molecular and Cellular Proteomics, 11(6).

  • Amy Claydon, Michael Thom, Jane Hurst and Robert Beynon (2012). ‘Protein turnover: measurement of proteome dynamics by whole animal m.etabolic labelling with stable isotope labelled amino acids’. Proteomics, 12(8), 1194-206

  • Catherine Arden, John Petrie, Susan Tudhope, Ziad Al-Oanzi, Amy Claydon, Robert Beynon, Howard Towle and Loranne Agius (2011) ‘Elevated glucose represses liver glucokinase and induces its regulatory protein to safeguard hepatic phosphate homeostasis’ Diabetes, 60(12), 3110-20.

  • Sheona Drummond, John Hildyard, Helena Firczuk, Onrapak Reamtong, Ning Li, Shichina Kannambath, Amy Claydon, Robert Beynon, Claire Eyers, John McCarthy (2011) ‘Diauxic shift-dependent relocalisation of decapping activators Dhh1 and Pat1 to polysomal complexes’ Nucleic Acids Research, 39(17), 7764-74.

  • Amy Claydon and Robert Beynon (2011) ‘Protein turnover methods in single-celled organisms: Dynamic SILAC’. In, (Castrillo, J. I. and Oliver, S. G., Eds.) ‘Yeast System Biology’. Methods in Molecular Biology (MiMB) series, 759, 179-195. (Series Ed: Walker, John M. ISSN: 1064-3745). Humana Press. Springer, New York.

  • Philip Brownridge, Luciane Vieira de Mello, Mary Peters, Lynn McLean, Amy Claydon, Andrew R. Cossins, Phillip D. Whitfield and Iain S. Young (2009) ‘Regional variation in parvalbumin isoform expression correlates with muscle performance in common carp (Cyprinus carpio)’ Journal of Experimental Biology, 212, 184-193.