Enhanced and robust characterisation of dynamic protein post-translational protein modifications


Post-translational modification (PTM) of proteins is an essential means of allowing rapid regulation of protein function in all organisms. This process, which is typically reversible and extremely dynamic, allows cells to respond rapidly to environmental factors, be that e.g. growth factors, stressors, or contact adhesion with other cells. Consequently, dys-regulation of PTM status can cause of disease, including e.g. cancer, diabetes and auto-immune disorders, and often drives diseases e.g. infection. To understand how different types and sites of protein PTM contribute both to fundamental and disease biology, it is essential to catalogue these PTMs in a high-throughput manner across the whole protein complement, and quantify how they are regulated under different conditions. However, the vast majority of PTM discovery studies focus on specific types of modifications, particularly phosphorylation of serine, threonine and tyrosine residues. Recent technology development in our group has revealed that many other amino acids are also phosphorylated on human proteins and suggests that there is extensive interplay between different types of PTM on the same residues.

This PhD studentship will join an exciting collaborative partnership between Prof. Claire Eyers, Prof. Andy Jones and Waters Corporation, one of the leading mass spectrometry instrument manufacturers, to develop advanced analytical and computational strategies to define and explore PTM diversity and interplay on human proteins. Using these methods, we will characterise the global PTM profiles in human model cell lines as a function of different cellular stressors and across the cell cycle looking at co-regulation of different types and sites of modification.

The supervisory team comprises:

·        Claire Eyers (Director, Centre for Proteome Research, https://www.liverpool.ac.uk/cpr/; Twitter: @ClaireEEyers) – https://www.liverpool.ac.uk/integrative-biology/staff/claire-eyers/

·        Andy Jones (Director, Computational Biology Facility, https://www.liverpool.ac.uk/computational-biology-facility/; Twitter: @andy___jones) – https://www.liverpool.ac.uk/integrative-biology/staff/andrew-jones/

You will join an established collaboration between the groups of Eyers and Jones, and benefit from a formalised collaboration with Waters. You will receive broad training in mass spectrometry-based proteomics, computational biology, and cell signalling. Specific training will be provided in fundamental mass spectrometry, the associated computational analysis tools for protein/proteomics data and pathway interrogation, and basic cell biology, making you highly employable across the field of biological sciences.

Whilst predominantly based in Liverpool, where you will join a dynamic and collaborative group of research scientists, you will also spend time at the Waters development site in Wilmslow. It is expected that the outcomes of this research will likely lead to several high impact publications and conference presentations.


Applications should be made by emailing  with:

·        a CV (including contact details of at least two academic (or other relevant) referees);

·        a covering letter – clearly stating your first choice project, and optionally 2nd ranked project, as well as including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project(s) and at the selected University;

·        copies of your relevant undergraduate degree transcripts and certificates;

·        a copy of your IELTS or TOEFL English language certificate (where required);

·        a copy of your passport (photo page).

A GUIDE TO THE FORMAT REQUIRED FOR THE APPLICATION DOCUMENTS IS AVAILABLE AT https://www.nld-dtp.org.uk/how-apply. Applications not meeting these criteria may be rejected.

In addition to the above items, please email a completed copy of the Additional Details Form (as a Word document) to . A blank copy of this form can be found at: https://www.nld-dtp.org.uk/how-apply.

Informal enquiries may be made to 

The deadline for all applications is 12noon on Monday 9th January 2023. 




Open to students worldwide

Funding information

Funded studentship

CASE studentships are funded by the Biotechnology and Biological Sciences Research Council (BBSRC) for 4 years. Funding will cover tuition fees at the UK rate only, a Research Training and Support Grant (RTSG) and stipend. We aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.



(2022) Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. J Proteome Research 21, 6, 1510–1524
(2022) Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. J Proteome Research 21, 1603-1615
(2019) Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation. EMBO J 38:e100847 doi.org/10.15252/embj.2018100847
(2017) Evaluation of parameters for confident phosphorylation site localization using an orbitrap fusion tribrid mass spectrometer. J Proteome Research 16:9 3448-3459
(2018) Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants. Journal of Proteomics 181, 152-159