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Core Team
Ben Collins Group Leader	Ben is the Professor of Proteomics and Chemical Biology in the School of Biological Sciences at Queen’s University Belfast, UK. His research focuses on broadly on 3 topics: (i) method development and applications in data independent acquisition mass spectrometry; (ii) analysis of protein interaction networks and protein complexes; and (iii) applications of these strategies in drug discovery, innate immunity, host-pathogen biology, and cancer biology. Ben’s PhD was completed at University College Dublin in 2009 where he remained for 1 year as the Agilent Technologies Newman Fellow. Ben moved to the Institute of Molecular Systems Biology at ETH Zurich in Autumn 2010 as postdoctoral researcher in the pioneering group of Prof. Ruedi Aebersold, where his research focused on the application of quantitative interaction proteomics in signaling and the development of DIA mass spectrometry. Following this Ben was a Group Leader and SNF Ambizione Fellow at ETH Zurich before moving to Belfast in 2019 to set up an independent group. In 2020 Ben won the HUPO Discovery in Proteomic Sciences Award for contributions to DIA mass spectrometry. He currently co-directs the NI Centre of Excellence for Chemoproteomics.
Mohammad Arefian Postdoctoral Research Associate	I obtained my Ph.D. from Ferdowsi University of Mashhad, Iran in 2018; wherein I evaluated the effect of salinity stress on plants at physiological, gene expression, and proteome levels. I continued my research as a Postdoctoral Fellow at Yenepoya research center in India, where my research mostly focused on kinase-mediated signaling pathways (de)activated in rice and Arabidopsis upon stress and during flowering. Besides post-translational modifications, my researches were also involved proteomic, proteogenomic, and metabolomic approaches to investigate cancers and infectious diseases in human, as well as stress-responsive mechanisms in model plants.
Chinmaya Narayana Postdoctoral Research Associate	Chinmaya is a mass spectrometry enthusiast with over seven years of experience working with various LC-MS systems. His journey with mass spectrometry began at Aurigene Discovery Technologies in Hyderabad, where he spent nearly two years as a research associate in the drug metabolism and pharmacokinetics team. He then pursued his Ph.D. at Yenepoya Research Centre, Yenepoya University in Mangaluru, India, focusing on developing a mass spectrometry-based species-specific spectral library for non-tuberculous mycobacteria under the guidance of Prof. T. S. Keshava Prasad. Upon completing his Ph.D., he joined the Collins Lab at the School of Biological Sciences, Queen’s University Belfast, as a post-doctoral research fellow. Chinmaya’s technical expertise includes handling and maintaining various LC-MS systems, as well as developing and optimizing methods such as PRM, MRM, DIA, and DDA for peptides, small molecules, and intact proteins.
Emma Mckay PhD Student	Project: Protein complex dynamics in innate immunity. Emma is a PhD student investigating the dynamics of protein interactions and post translational modifications in the NLRP3 inflammasome system, a central signalling hub of the innate immune system. Emma completed her undergraduate degree in Biological Sciences at Queens University Belfast, graduating in 2021. Co-supervisor Rebecca Coll
Dino Rocca PhD Student	Project: Regulation of Inflammasome Function by the Ubiquitin System. Dino received his degree in Biotechnology from the University of Galway. During this time, he carried out a seven-month research placement at Leiden University Medical Centre in the Netherlands, where he investigated the pathogenic and non-pathogenic effects of protein aggregation in OPMD cell models. For his final year project, he conducted another research placement at the Centre for Chromosome Biology Galway where he utilised shRNA technology to down regulate proteins of interest related to CDC7 and DNA replication. Dino’s PhD will investigate the regulation of inflammasome function by the ubiquitin system. Co-supervisors Helen Walden and Rebecca Coll
Knox Wilson PhD Student	Project: Advanced Mass Spectrometry to Expand the Chemical Proteomics Toolset. Knox completed his undergraduate degree in biochemistry from Queen’s University Belfast in 2024. For his final year project, he was interrogating protein:protein interactions of the ubiquitin system by analysis of affinity purification mass spectrometry data. His PhD aims to advance mass spectrometry to expand the chemical proteomics toolset. Co-supervisor Dan Longley and Rich Williams
Thomas McConnell PhD Student	Project: New Chemoproteomics Tools for Drug Discovery in Inflammation. Thomas earned his Bachelor’s degree in Molecular Genetics from the University of Dundee, where he also completed an exchange semester at the National University of Singapore, with a focus on genetic medicine. For his Honour’s project, he worked under Professor Yogesh Kulathu at the MRC Protein Phosphorylation and Ubiquitylation Unit. There, he developed a novel model cell line to characterise UFM1-specific proteases using a targeted protein degradation approach. He then pursued a Master’s degree in Experimental Medicine at Queen’s University Belfast, working under Dr. Rebecca Coll and Dr. Rich Williams. His research involved synthesising and evaluating the functionality of novel sulfonamide compounds to inhibit the NLRP3 inflammasome. Currently, for his PhD, Thomas aims to use chemoproteomic tools to study inflammasome components and screen for druggable targets. Co-supervisor Rebecca Coll
Niamh Mallon Msci Student	Project: Characterizing small molecule induced protein-proteins by affinity purfication-mass spectrometry
Co-Supervision
Simran Cheema PhD Student	Project: Maximizing the clinical impact of Human Milk on Prevention of Necrotizing Enterocolitis. Co-supervised with Simon Cameron and Natalie Shenkar
Daniel Lockwood PhD Student	Subversion of innate immune defences by intracellular bacterial pathogens. Co-supervised with Gunnar Schroeder and Miguel Valvano
Prachi Bendale PhD Student	Novel Molecular Tools to Tackle the Antimicrobial Resistance (AMR) Emergency. Co-supervised with Gerd Wagner and Miguel Valvano
Reem Elasad PhD Student	Targeting Transcriptional Drivers of Resistance in Colorectal Cancer. Co-supervised with Simon McDade

Alumni
Jack Penny PhD graduated 2024 (QUB)	Mass Spectrometry method development to investigate the ubiquitin-like protein modifier ISG15
Charlotte Nicod PhD graduated 2020 (ETH Zurich)	Unraveling host-pathogen interactions upon Mycobacterium tuberculosis infections using quantitative mass spectrometry. Now Associate at Flagship Pioneering.
Amir Banaei-Esfahani PhD graduated 2019 (ETH Zurich)	Deconvolution of Biochemical Pathways in Genetically Diverse Mycobacterium tuberculosis. Now Senior Bioinformatics Scientist at Universitätsspital Zürich.
Shruti Jha Research Assistent 2017-2019 (ETH Zurich)	Host-pathogen interactions upon Mycobacterium tuberculosis infections. Now Research Associate at DewPoint Therapeutics.

Project Students
Cormac Mathews BSc Student 2024	Inference of splice isoforms in the inflammasome from global mass spectrometry proteomics data
Caoimhe Lynch BSc Student 2024	Assembly of a p97 cofactor protein-protein interaction network.
Elmoatasm Omar BSc Student 2024	Assembly of a Mycobacterium tuberculosis host-pathogen protein-protein interaction network from affinity purification mass spectrometry data.
Ellie Schevlin BSc Student 2024	Proteome analysis of macrophages infected with Mycobacterium tubercolosis RD1 mutant.
Knox Wilson BSc Student 2024	Assembly of a p97 cofactor protein-protein interaction network from affinity purification mass spectrometry data.
Sophia Kennedy BSc Student 2024	Novel post translational modifications in the 14-3-3 signalling system.
Jie Ma MSc Student 2023	Analysis of Protein Complex Alterations of Immune System in using SEC-SWATH Mass Spectrometry.
Ciaran Purdy BSc Student 2023	Proteome analysis of macrophages infected with Mycobacterium tuberculosis RD1 mutant.
Abbie McDougall BSc Student 2023	Identifying Novel Post Translational Modifications in Blood Plasma Proteins.
Meaghan King MSc Student 2022	Assembly of a Mycobacterium tuberculosis host-pathogen protein-protein interaction network.
Olivia Mulderrig BSc Student 2022	Novel post translational modifications in cardiomyopathy.
Daniel Cosby BSc Student 2022	Novel post translational modifications in the VCP/p97 signalling system.
Katie Marshall BSc Student 2022	Epitope mapping of cell surface proteins of Mycobacterium tuberculosis complex organisms.
Cansu Uygun MSc Student 2021	Mass spectrometry based proteomics – longitudinal evaluation and quality control of analytical methods.
Noemi Casaferniza Ochoa MSc Student 2021	Novel post translational modifications in the interactome of 14-3-3β.
Clare-Ann Nelson BSc Student 2021	Novel Post Translational Modifications in the Macrophage Proteins Targeted by Mycobacterium tuberculosis.
Emily Lecky BSc Student 2021	Quantitative Aspects of Ion Mobility – Mass Spectrometry in Proteomics.
Megan Taylor BSc Student 2021	Proteome analysis of macrophages infected with Mycobacterium tuberculosis RD1 mutant.
Caolán Doran MSc Student 2020	Assembly of a p97 cofactor protein-protein interaction network.
Jun Cai MSc 2018 (ETH Zurich)	Elucidating Host-Pathogen Protein-Protein Interactions in the Context of Mycobacterium Tuberculosis Infections.