Institute for Cell and Molecular Biosciences

Staff Profile

Professor Matthias Trost

Professor of Proteomics


Matthias Trost studied chemistry in Freiburg, Germany and Manchester, UK. He received a Ph.D. in 2004 from the Helmholtz Centre for Infection Research, Braunschweig, Germany, for research on the proteome of the human pathogen Listeria monocytogenes and Listeria infected host cells. Matthias then carried out postdoctoral research with Michel Desjardins and Pierre Thibault at the University of Montreal, Canada, working on the proteome and phospho-proteome of the phagosome.


In 2010, Matthias became Programme Leader and Head of Proteomics in the MRC Protein Phosphorylation and Ubiquitylation Unit at the University of Dundee, Scotland, UK. Since 2017 he is Professor of Proteomics in the Faculty of Medical Sciences at Newcastle University, UK.

Positions held:
Since 2016   Professor of Proteomics, Newcastle University, Newcastle-upon-Tyne
2010-2017    Programme Leader (PI) and Head of Proteomics at the MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland
2006-2010    Post-Doctoral Position, later Research Associate with Pierre Thibault, Institute in Research in Immunology and Cancer (IRIC), Montréal, Canada
2005-2006    Post-Doctoral Position with Michel Desjardins, Université de Montréal, Canada

2001-2004     PhD in Cellular Microbiology & Proteomics (Supervisor:  Lothar Jänsch & Jürgen Wehland, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany): “Functional genome analysis of secretory proteins and the Host-Pathogen-Interactions of the human pathogen Listeria monocytogenes”
2001        Diploma in Chemistry, Thesis in the group of Peter Gräber (Biophysical Chemistry, University of Freiburg): ‘The H -ATP-Synthase of Escherichia coli’.
1995-1996     BSc (Hons.) in Chemistry at the University of Manchester in Science and Technology (UMIST) (now: University of Manchester), Third Year Project: Analysis of peptide mixtures by MALDI TOF MS (Supervisor: Simon J. Gaskell, Michael-Barber-Centre for Mass Spectrometry)
1993-2000    Study of Chemistry at the University of Freiburg, Germany

Area of expertiseProteomics, Innate Immunity, Macrophages, Phagosome, Post-translational modifications

Google scholar: Click here.



Mass spectrometry (MS)-based proteomics has developed at an astonishing pace over the last 20 years. This progress is largely due to the development of new powerful mass spectrometers. However, sample preparation, chromatography as well as data analysis and visualisation have not kept up with this development and new tools in these areas are required in order to utilise the potential of these mass spectrometers. A particular problem is that many proteomes display a very wide range of protein concentrations between high-abundance and low-abundance proteins sometimes in the order of 108 or even higher. In human serum for example, 10 proteins make up 90% of the protein content. Unfortunately, most mass spectrometers are physically limited to a linear dynamic range of ~103. To overcome this technically challenging problem, samples need to be fractionated by an additional chromatographic step.

My lab has in recent years focussed on developing and establishing proteomics techniques that allow us to answer important biological questions. Our published work was directed towards two aims: 1. Increasing the number of proteins identified in proteomics experiments whilst keeping or reducing the sample amount and instrument time. 2. Developing a MALDI TOF mass spectrometry-based assay to characterise chain specificity and activity of deubiquitylases (DUBs).  

Understanding Phagosome Biology

The biological focus of my lab is on macrophage innate immune responses and phagosome biology. Macrophages are highly diverse and plastic immune cells that can polarise in response to environmental cues into many different phenotypes. The two best characterised functional phenotypes are the inflammatory M1 phenotype “classically” activated through Toll-like receptor (TLR) agonists and interferons, and the anti-inflammatory M2 phenotype “alternatively” activated through interleukins-4 or 13 which are secreted during wound-healing and parasite infections. However, given the fact that macrophages possess regulatory receptors for a bewildering array of growth factors, cytokines, chemokines, prostanoids, etc., this binary divide is intrinsically unlikely. A more sustainable view sees macrophage polarization more in the nature of a much broader multi-dimensional model.2 Moreover, there is a huge diversity of tissue-resident macrophages with important and diverse functions in virtually every human organ, for example microglia in the brain, Kupffer cells in the liver and the three different described subsets of macrophages in the lymph node. Because of their importance and this diversity, it is not surprising that dysregulated macrophage polarization is frequently associated with disease.
Macrophages are important phagocytes that clear apoptotic cells and cellular debris during development and tissue homeostasis as well as pathogenic microbes during infection. Phagocytosis can be defined as the uptake of large particles (~0.5-10 ?m) by cells. It is an important cellular mechanism for all eukaryotes and highly conserved in evolution: while lower eukaryotes phagocytose for food, multicellular organisms have developed specialized phagocytic cells such as macrophages as a key part of the innate immune response. Phagocytosis is induced through binding of particles as diverse as inert beads, microbes or apoptotic cells to a variety of cell surface receptors. After internalization, newly formed phagosomes engage in a maturation process that involves fusion with endosomal populations and ultimately with lysosomes, leading to the formation of phagolysosomes where the foreign matter within is degraded. Microbe degradation in the phagosome produces antigens, which are presented at the cell surface to activate specific lymphocytes and elicit appropriate immune responses, linking innate to adaptive immunity.
Phagosomes are highly complex organelles that are in constant change due to fission and fusion with other organelles. The use of latex or polystyrene beads as inert baits for phagocytosis enables the purification of highly enriched phagosomes. Proteomics analyses on these pure phagosome fractions revealed contributions of the endoplasmic reticulum (ER) to the phagosomal membrane and its consequences on MHC class I peptide cross-presentation. In my post-doc, I analysed latex bead phagosomes of resting and interferon-? (IFN-?) activated macrophages, showing – among other things - that antigen presentation is preferred over fast microbe degradation in activated macrophages.
Our understanding of phagosome biology is of great importance as several pathogens including Leishmania, Brucella and Legionella species, and, most prominently, Mycobacterium tuberculosis are able to subvert phagosome maturation allowing them to survive as intracellular pathogens. In particular tuberculosis has been identified as a major global health threat by the World Health Organisation (WHO)16 with 9.4 million incident cases, 14 million prevalent cases and 1.68 million deaths in 2009 alone, highlighting the importance of our understanding of phagosome function during infection.
Moreover, phagosomal, endosomal and autophagosomal delivery to the lysosome is controlled by the same vesicular trafficking complexes. But while phagosomes can be isolated to a high purity, endosomes and autophagosomes cannot. This offers a unique chance to characterise conserved principles in these pathways employing proteomics, cell biological and biochemical tools. It will give insights into broader biological contexts such as many neurodegenerative diseases that are caused by mutations in proteins important for lysosomal delivery.
The key questions we want to understand are how proinflammatory signals are transduced from the phagosome and how proinflammatory activation regulates vesicle trafficking of the phagosome. We focus our studies on characterising the roles of ubiquitylation and phosphorylation in these pathways and to understand the molecular details of immune responses and how the phagolysosomal destruction of phagocytosed prey is orchestrated.



I teach once a year a post-graduate course on the basics of mass spectrometry and proteomics.