Biomedical Proteomics Research Group

Group Overview

The Biomedical Proteomics Group has been working for a number of years to develop capability for advanced protein discovery using mass spectrometry and has forged strong collaborative links with clinical colleagues, locally and internationally.
We are currently working on a range of diseases including Prostate Cancer, Psoriatic Arthritis and other related inflammatory conditions, Heart Failure and Diabetes. Housed in the UCD Conway Institute our team encompasses lab-based scientists, statisticians, visiting fellow and of course clinicians.

Pennington + Watson Groups - 580 x 406

The Pennington & Watson Research Groups


Group Information

Location: UCD Conway Institute
PI: Prof Stephen R Pennington



Steve graduated from Imperial College of Science and Technology (University of London) with a joint honours degree in Chemistry and Biochemistry (upper second) before completing a PhD in Biochemistry at the University of Cambridge.  During his PhD he was awarded an Elmore Medical Research Fellowship.  It was during this fellowship that his interests in the regulation of the mammalian cell cycle began, the subject of his research that was continued when he moved the Department of Human Anatomy & Cell Biology at the University of Liverpool to take up a post as a Wellcome Trust funded lecturer.  Subsequently he was a University Lecturer and then Senior Lecturer.  During this period his research included the use of two-dimensional gel electrophoresis (2-DE) which was subsequently combined with mass spectrometry for protein characterisation.  Steve has been active in the practical implementation of collaborative proteomics projects and set up a multi-user proteomics facility at the University of Liverpool that served as a 'prototype' for the facility he established when he moved to the Conway Institute in 2003. Stephen¿s vision for the development of proteomics in UCD has been to use his expertise and experience to apply proteomics (in its broadest definition) to a diverse range of research programmes. Of particular interest to Steve's is the development of translational clinical translational projects that align research results to the clinical setting and the development of methods for the discovery and subsequent quantitative measurement of proteomic biomarkers.

Prof Steve Pennington - 260 x 325

Professor Stephen R Pennington

Professor of Proteomics

Steve has received a Sir Henry Wellcome Commemorative Award for Innovative Research, has been Director of Research and member of the Board of a Cambridge-based seed-corn funded fledgling biotech company and has served in small scale consultancy capacities for a number of commercial organizations. He has given many presentations in the UK, Europe, the US and Asia including two industry funded lecture tours of Asia where he gave presentations in Taiwan, South Korea, Hong Kong and mainland China.

He is on the editorial board of several journals including in a more senior capacity for 'Proteomics' and the 'Journal of Proteomics' and regularly reviews manuscripts and grants for a number of international organisations.

Dr Brian Flatley                                         
Post-Doctoral Research Fellow

Dr Lisa Staunton                                          
Post-Doctoral Research Fellow

Berlinda Hernández
PhD Student

Claire Tonry                              
PhD Student

Anna Kwasnik                                      
PhD Student

Matthew Doyle                            
PhD Student

Darren Doherty                                      
Research Assistant

Opeyemi Stella Ademowo                                      
Research Assistant

Cathy Rooney                                     
Senior Research Technician

I completed my PhD in the University of Reading under the joint supervision of Prof. Rainer Cramer (University of Reading) and Mr Peter Malone (Harold Hopkins Department of Urology, Royal Berkshire NHS Foundation Trust Hospital). The remit of the research study was "Utilisation of mass spectrometry in the quest for male urogenital protein biomarkers".

The two main areas of research focus was the exploration of detection methods for differentiating prostate cancer from other non-malignant diseases/infections that improve upon current tests using prostate specific antigen levels in the blood as an indicator and secondly employing mass spectrometry imaging techniques to visualise protein distribution across normal and malignant tissue removed from men diagnosed with penile cancer.

In 2013 I moved to University College Dublin to take up a position as a Postdoctoral research fellow funded by the Movember Serum Global Action Plan. Here my work is focussed on the development and validation of a new MRM-MS assay for aggressive prostate cancer.

I received my PhD from the National University of Ireland Maynooth in 2011 where my project focused on the proteomic profiling of animal models of myotonia and motor neuron disease.

In 2012 I moved to the University College Dublin to take up the position of post doctoral research fellow funded my the Health Research Board (HRB). My project aims to identify the protein expression profiles of morphologically discrete foci in prostate cancer using a clinically focused strategy for discovery of biomarkers.

My project is focused on distinct regions of cancer foci in tissue from patients which are isolated by laser capture microdissection and proteomic profiling by label-free LC-MS/MS to identify differential expression both between regions and patient groups followed by multiplexed measurement of proteins of interest by MRM mass spectrometry.

I am currently studying for a PhD entitled “Integration of transcriptomic and proteomic data for selection, measurement and classification of potential prostate cancer biomarkers” under the supervision of Dr Andrew Parnell and Prof Stephen Pennington. 

My research interests include Bayesian analysis, classification and machine learning models for biomarker discovery as well as methods for dealing with missing data. To date I have been researching model based machine learning methods and developing new methods to find predictive biomarkers in proteomic data, with a focus on predicting the severity and recurrence of prostate cancer. I have also been involved in researching current and new techniques for dealing with missing data.

I am currently completing a Research Masters with the Pennington Group. My research has been focused on the design of robust MRM assays for a panel of 26 candidate biomarker proteins of Cardiovascular Disease. The abiltity of this panel to predict Heart Failure was verified via analysis of the of 500 non-depleted patient serum samples. This sample was composed of both Heart Failure (150) and non-Heart Failure (350) patients. Quality Control samples were used to monitor instrument performance throughout this large-scale MRM-based investigation and also to subsequently normalize the resulting data for variants within batches and across all batches of patient samples.


This coming September I will be embarking upon a PhD with the Pennington group. The focus of this PhD will be on proteomic analysis of prostate cancer patient response to treatment. Similar techniques will be employed here for the development of robust MRM assays for a bioamerker signature for prediction and monitoring of patient response to combined hormonal and radiation therapy. A critical need for such research arises in the fact that many patients fail treatment after a certain period of time. With a sample cohort collected as part of a clinical trial, we will be able to use mass-spectrometry-based analysis to monitor proteomic changes occurring in patients through the course of their treatment. Of this cohort, a proportion of samples will belong to patients who will fail therapy. With proteomic interrogation of such samples, we aim to identify a protein biomarker signature, which can be used for early prediction of treatment failure and improved monitoring of patient response to treatment over time.

Recently, I completed a research Master thesis undertaken in the UCD Conway Institute and registered in the School of Medicine and Medical Science. The main goals of the project were to confirm the interaction between the transcription factor SREBP and the adaptor protein HP1 as well as investigate potential functional consequences of this interaction. Additionally, the importance of specific amino acids on the post-transcriptional modification of SREBP during mitosis and its role in the transcriptional activity of SREBP were investigated.

I am currently studying for a PhD project entitled “An ‘omics strategy for targeting cell proliferation” under the supervision of Professor Stephen Pennington. Using transcriptomic and proteomic technologies, we hope to gain a better understanding of how cell division in human cells is regulated by Ca2+ signalling and how we can manipulate this regulation for intervention in many diseases.

I am currently studying for my PhD entitled “Act1 (TRAF3IP2) in Psoriatic Arthritis: The effect of disease associated gene variants on Act1 protein interactions and signalling pathways” under the supervision of Prof.  Stephen Pennington and Prof. Oliver FitzGerald.

My current project is directed towards using an unbiased proteomics approach combined with a targeted hypothesis driven strategy to establish the effect of disease associated gene variants of the TRAF3IP2 gene on the protein interactions of its encoded protein Act1 and downstream inflammatory signalling pathways in psoriatic arthritis.

The techniques that I have used include western blotting, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), plasmid isolation, complex-immunoprecipitation, cell culturing, cell transfection, bacterial propagation, bacterial transformation and in-gel tryptic digestion of cell culture lysates for LC-MS/MS.

The newest member of the lab, I am currently involved in the development of a bio-repository in conjunction with St. Lukes hospital. This bio-repository will be used to store clinical trial samples for use in future proteomic studies. 

In the near future I will be involved in the development and validation of protein biomarkers which are indicative/ prognostic of hormone treatment failure in prostate cancer patients. These markers will be validated using Multiple Reaction Monitoring.

Inflammatory arthritis is associated with autoimmunity. It is characterised by autoantibodies in the systemic fluid and tissues. Examples include rheumatoid arthritis (RA) and psoriatic arthritis (PsA). TNF-α, a key cytokine that drives the inflammatory and destructive processes of these diseases is a common target for therapeutic intervention and some of the most effective recent treatments include ‘biologicals’ to target these pathways. However, not all patients respond to TNF-α inhibitors and those who do respond show diverse degrees of response. Treating patients with potentially ineffective biologicals is time consuming, expensive and carries a number of unwanted side-effects. During my PhD, the protein expression in the synovium (joint tissue) of PsA patients before treatment who subsequently respond or did not respond to anti-TNF-α drugs was investigated and compared. A candidate protein biomarker panel was established and used to predict response to treatment in an independent cohort by measuring the proteins with targeted proteomics using multiple reaction monitoring (MRM) assays.

In my current role, I am trying to develop MRM assays for a 50-biomarker panel of serum proteins from prostate cancer (PCa). PCa is the most commonly diagnosed cancer in men in the US and Europe. PCa incidence has increased significantly in the last 20+ years and it is the third major cause of cancer death in Ireland. This is a Movember project and Movember is a part of the Prostate cancer Global Action Plan; a collaboration to develop an integrated panel of blood biomarkers that could help distinguish indolent from aggressive disease. This project aims to better predict aggressive PCa, characterise disease and treatment resistance by identifying clinical biomarkers that may ultimately enhance clinical decisions.

I recently finished my PhD in Rheumatology where I discovered and developed a protein biomarker panel potentially capable of predicting treatment outcome to biologic therapy in inflammatory arthritis. I used label-free proteomics and multiple reaction monitoring (MRM) assays for the discovery and verification of the biomarkers. I love innovation, discovery, and knowledge acquired through science.

Presently, I am working on a Movember project on Integrated Global Serum Biomarker (MRM-MS based quantification of 50-panel prostate cancer serum proteins using the standard flow uHPLC coupled to a 6490 triple quadrupole mass spectrometer) and assisting to set up a new mass spectrometer lab equipped with a new Agilent 6490 triple quadrupole mass spectrometer for MRM development.

I have been working in the mass spectrometry field since 2001, when I worked on the development and analysis of prostaglandins by MRM for various clinical studies while working at the Royal College of Surgeons. In 2008 I moved to UCD to take up a senior technician post with Steve, Mike Dunn and the MSR facility. Since September 2011, I have predominately been working on the Prostate Cancer Research Consortium- Work Package 4.

The aim of this project is to identify peptide biomarkers capable of distinguishing aggressive/significant  prostate cancer from the indolent disease. Validation of this panel is on-going presently using MRM methods on our Agilent 6460 triple quadrupole.

I also am involved in training staff and students on the operation and trouble-shooting of our Agilent instruments.

I carry out the mass spectrometry analysis for several other projects within the Conway Institute and also for some external collaborators, the most recent of whom include System Biology Ireland (SBI) and Dr. Angela Malley of Universitat Wurzburg, Germany.


Project Title


Grant Funding

Belinda Hernanadez

Integration of transcriptomic and proteomic data for selection, measurement and classification of potential prostate cancer biomarkers

Andrew Parnell

Irish Research Council

Stella Ademowo

Discovery and Development of Protein Biomarkers to Predict Response to Biologic Therapy in Inflammatory Arthritis



Integrated Global Serum Biomarkers of prostate cancer (MRM-MS based quantification of 50-biomarker panel of serum proteins from prostate cancer)

Prof. Oliver FitzGerald







Prof. Bill Watson

Rheumatology Dept. St. Vincent’s University Hospital Dublin




Movember ( A part of Pca Global Action Plan)

Claire Tonry

Development of MRM assays for measurement of biomarker panel of CVD

Dr. John Baugh,

Dr. Chris Watson

Enterprise Ireland

Claire Tonry

Proteomic analysis of prostate cancer patient response to treatment: development of a protein biomarker panel to predict and monitor response to combined and radiation therapy

Prof. John Armstrong

 St. Luke's Hospital

Lisa Staunton

Protein Expression profiles of morphologically discrete foci in prostate cancer

Prof Orla Shiels

Dr. Sharon O’Toole

Dr. Peadar O’Gara

Health Research Board

Darren Doherty

Proteomic Analysis of Combined Hormonal Therapy and Radiation Therapy for Localised Prostate Cancer

Prof. John Armstrong


St. Lukes Hospital


UPMC Beacon Hospital


Irish Co-operative Oncology Research Group (ICORG)

Cathy Rooney

Protein Expression profiles of morphologically discrete foci in prostate cancer



 Health Research Board

PI Markers - Bringing Biomarkers to Another Level

In conversation with Claire O'Connell

If you want to know more about a patient’s state of health, a quick tick on a form can order a lab test to measure levels of a particular  molecule - often a protein - in the patient’s blood. And in some cases of cancer, perhaps measuring the levels of a protein in a tumour could  help to tailor the treatment for that particular patient.

Biomarkers offer  valuable clues for clinicians, and Prof Steve Pennington is looking to develop new approaches to help translate fundamental discoveries about  potential biomarkers into the validated, useful tests behind the ticks on forms. 

Currently Professor of Proteomics in UCD School of Medicine and Medical Science, Stephen has long-standing expertise in biomarker discovery, which involves measuring and comparing levels of proteins in patient  samples to identify molecules that could give some insight into a patient’s current disease state, response to a treatment or likely progression.

But while identifying those proteins of interest is a start, Prof Pennington has recently been focusing on a more translational push towards a clinical diagnostic application.

“What I would like to see come out of the  discovery work we have done is a tick box on one of those forms a clinician fills in to say they need a test done,” he explains. “And to do that you need to be able to confirm that these [biomarker] changes occur in the patient cohort you have been working with, in a new patient cohort and  then Into even larger patient cohorts. Plus it has to be a test that clinicians need, and that someone will drive from a commercial standpoint.”

Prof Pennington’s team have been working on new approaches to analysing proteins in  patient samples, and they are particularly interested in using triple quad  mass spectrometry.

“We have been developing a new approach to doing very targeted proteins measurements in the mass spectrometer,” he explains.  “So rather than asking the mass spec to see as many proteins as it  possibly can and looking for differences between samples, this new  approach using the triple quad asks the mass spec to measure only  proteins of interest.”

He can now use  triple-quad mass spectrometry to measure 50 to 100 proteins  simultaneously and semi-quantitatively in a patient samples.

“In this  way we can confirm that changes we find in ‘discovery experiments’ are  authentic in large patient cohorts,” he says. “And ultimately I would  see that the triple quad mass spectrometer would be the the instrument  that would analyse the samples in a clinical diagnostics lab. The idea  of this sophisticated machine being a turnkey device was initially met  with resistance, but these assays are really robust, they have the  reproducibility required and some clinical labs already use them.”  

Earlier this year, Prof Pennington’s lab signed a partnership agreement  with Agilent Technologies, which means the only triple-quad mass  spectrometer of its kind in Europe is now housed in a controlled environment at the Conway Institute. “Agilent is supporting that  instrument so we can  demonstrate its performance to their potential customers,” he explains.

Prof  Pennington is now using the UCD facility to develop biomarker assays  more suited to the commercial and clinical diagnostic environment,  particularly in prostate cancer and arthritic disease. 

His lab was recently awarded grant of €250,000 euro from SLICR to  continue work on prostate cancer biomarkers with Prof John Armstrong at  St Luke's Hospital in Rathgar, and Prof Pennington is also teaming up  with Prof William Watson in UCD as part of a global initiative (GAP) funded by the Movember Foundation, which is bringing together the efforts of  research groups from the US, Europe, Canada and Australia.

“In the GAP we want to take all of the biomarker candidates that groups from around the world have found and prioritise them, so we can identify which of  them are potentially the most likely to suit specific clinical  questions,” says Prof Pennington, who explains that collaborating to  increase the numbers of samples and biomarkers increases the odds of  finding viable candidates. “Our feeling is that if instead of measuring 3 or 4 potential candidate biomarkers, if you measure 300 or 400 then it  improves your chances. And the value of the mass spec approach is  that If you measure 300 things it doesn’t cost you much more than  measuring 100, other than a few minutes on the instrument.”

It’s not just prostate cancer that stands to benefit: Prof Pennington also has an  interest in biomarkers for arthritic disease. Along with Prof Oliver  Fitzgerald at St Vincent’s University Hospital, he is working with  European partners on the EU-funded MIAMI project, a three-year  initiative to look for biomarkers in patients with arthritis that can  help predict complications of the disease, such as gut problems and  joint destruction. 

And more generally, he hopes that his lab’s links with industry will  build up a reputation of translating discovery into a more clinical  setting: “What I am looking forward to in the future is developing our  capability in a more commercially directed way.”