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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 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.
Jack Penny PhD Student	Project: A map of host cell rewiring by pathogens. Jack is a PhD student investigating host cell rewiring by pathogens with a particular interest in the ubiquitin system. Jack completed his undergraduate degree in Biochemistry and Master of Research at Aberystwyth University in 2018. His previous projects involved metabolomics and natural product drug discovery with an interest in antimicrobials and overcoming resistance mechanisms. Co-supervisors Gunnar Schroeder and José Bengoechea
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. Starting Oct 2024. Co-supervisor Dan Longley and Rich Williams
Thomas McConnell PhD Student	Project: New Chemoproteomics Tools for Drug Discovery in Inflammation. Starting Oct 2024. Co-supervisor Rebecca Coll
Niamh Mallon Msci Student	Project: Characterizing small molecule induced protein-proteins by affinity purfication-mass spectrometry Starting Oct 2024
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

Alumni
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
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.