Mass Spectrometry Core

The UCD Conway Mass Spectrometry Core facilitates study of biomolecules that play important roles in fundamental and applied biology, particularly in health and disease. Our instruments enable use of state of the art proteomics and metabolomics approaches to address your scientific problem, including quantitative proteomics, post-translational modifications, and protein-protein interactions.

We work with academic, clinical, and industry partners; from novices to experienced researchers. Our team of experts are ready to listen to your research needs and offer dedicated strategic support at all stages of your project. Contact us using the details listed in the Team & Contact Details section below.

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The Mass Spectrometry Core is a state-of-the-art biologic mass spectrometry facility providing access to all the necessary instrumentation for high-throughput, high accuracy protein identification, quantification and characterisation.

In terms of equipment, the facility focuses on bottom up proteomics using the Thermo Fisher Q-Exactive mass spectrometer. Complex mixtures of peptides are separated using nano reverse phase C18 columns on an Dionex Ultimate 3000 UPLC connected to a Thermo Fisher QExactive mass spectrometer. This enables separation of complex mixtures of peptides, identification of peptides and their respective fragments as well as quantification based on peptide ion current. Typically, data dependent acquisition is carried out. However, users can also avail of data independent acquisition methods.


• MassSpec_Sample_Prep_General Guidelines
• MassSpec_In-Gel-Digestion

• MassSpec_In-solution-digestion
• MassSpec_FASP-Protocol

• Sample preparation: STAGE TIP clean up
• MassSpec_Sample preparation: Ziptip desalting


We can help guide you to the various stages of experiment analysis, including Protein Identification and Quantitation, statistical evaluation, data mining, and pathway analysis.
• MaxQuant (public domain)
• Mascot
• Perseus (public domain)
• Cytoscape (public domain)
• Skyline (public domain)

Gerard Cagney

Dr Gerard Cagney has extensive experience of mass spectrometry and proteomics, including leadership roles at UCD, UCSF and University of Toronto. He is expert in network biology, particularly protein interactions, and collaborates across many fields. 
Contact: gerard.cagney@ucd.ie

Caitriona Scaife

Caitriona has been with the Mass Spectometry Core facility since 2004. Formerly, she ran the 2DE Separations laboratory while more latterly she has worked on a number of large proteomics projects both in the wet-lab and on the subsequent data analysis. She has most recently been collaborating with Dr Jane English (University College Cork) and her team on hypothesis-driven analyses using targeted-data independent acquisition (DIA) for quantitation of protein targets.
Contact : T: (+353-1) 716 6916; E: caitriona.scaife@ucd.ie

Eugene Dillon

Eugene studied nutritional sciences in University College Cork before specialising in molecular nutrition during his MSc at Wageningen University. Eugene obtained an IRCSET Phd scholarship to work with Prof. Helen Roche and Dr Giuliano Elia utilising proteomics in the study of nutritional metabolism. After his PhD, Eugene worked as a postdoctoral scientist with Food for Health Ireland. Over the course of his doctoral and postdoctoral studies, Eugene has amassed expertise across sample preparation, mass spectrometric methodology, data processing and downstream pathway analysis.
Contact: T: (+353-1) 716 6835; E: eugene.dillon@ucd.ie