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This month we speak to Dr Marjorie Fournier, manager of the Advanced Proteomics Facility (APF) in the Department of Biochemistry about the facility's capabilities. The APF supports research and training activities in the field of mass spectrometry-based proteomics and is run by a team of expert scientists who support researchers from academia and industry on multidisciplinary research projects.

Widescreen photograph of the lab

Tell us a little about Advanced Proteomics Facility?

The Advanced Proteomics Facility (APF) is based in the Department of Biochemistry and supports research and training activities in the field of mass spectrometry-based proteomics. The facility is equipped with nano-liquid chromatography systems coupled with tandem mass spectrometers (LC-MS/MS), enabling comprehensive analysis of proteins in biological samples to elucidate molecular mechanisms governing cellular processes.

Our facility is run by a team of expert scientists to support researchers from academia and industry on multidisciplinary research projects. We operate on service and collaboration basis offering research support and training courses covering all aspects of a proteomics analysis, from experimental design to sample preparation, mass spectrometry analysis and bioinformatics analysis. Our mission is to provide high quality and meaningful proteomics data in a timely and cost-effective manner, and to train specialised and non-specialised scientists in the field of mass spectrometry-based proteomics.

Tell us a little about your role in the facility

Marjorie FournierMy role as the manager of the Advanced Proteomics Facility is, with the help of the proteomics team, to ensure high instrument performance, maintain cutting-edge proteomics technologies through methods development, and manage the finances of the facility, securing funding for instrument upgrade and research projects. I also communicate about our facility activity through participation in conferences, seminars and publications in peer-reviewed journals, and train our scientific community.

What are the capabilities of the facility?

The facility supports comprehensive proteomics applications from protein identification of complex biological samples to quantification and post-translational modifications analysis for functional proteomics analysis.

Typical projects aim to identify protein contaminants from protein purification, map protein-protein interaction or post-translational modifications on organelles or cellular proteomes, or identify protein abundance changes in cells or tissues in response to environmental changes (drug treatment, disease conditions, etc.). We also support structural proteomics analysis using cross-linking mass spectrometry, currently in high demand with the development of cryo-EM techniques.

Our facility is constantly evolving methods and applications through research activity. We also provide training to the next generation of researchers and give direct access to the instrument for our regular users. This gives a unique opportunity to learn about mass spectrometry techniques and instrument operations.

Why would our staff want to use the facility?

Our facility is run by a team of highly qualified researchers, specialised in the field of mass spectrometry-based proteomics. Our biological knowledge is key to understanding the biological questions of our researchers, to identify the most suitable proteomics methods, and for data interpretation. 

We aim to provide the best possible proteomics service to meet research projects requirements in a timely and cost-effective manner. We are based in the Science area of central Oxford which is convenient for facility access and communication with users.

Is there equipment available there that staff wouldn’t find elsewhere?

Aygul Malone and Daniel Molland, a Biochemistry DPhil studentWe are equipped with two types of nano-LC systems, Easy-nLC 1000 and Ultimate RSLC 3000, which can perform mono and multidimensional peptide separations. The nano-LCs are coupled in-line with three different types of mass spectrometers: an LTQ XL for sample quality check; three Qexactives (Orbitrap) which are the most sensitive instruments used for proteomics analyses of complex samples; and an Orbitrap Elite offering diverse fragmentations capacity (ETD, HCD) useful for PTMs mapping of complex samples.

Our proteomics data analysis suite is equipped with diverse software, MaxQuant/Perseus and Sequest/Proteome Discoverer for protein identification and quantification; PEAKS for de novo sequencing and post-translational modification analysis; Skyline and Pinpoint for targeted quantitation and Progenesis for label-free quantification; pLink for cross-linking mass spectrometry data analysis. We use R for statistical analysis and other online available software for functional annotation analysis.

Who do you collaborate with across the University?

The APF is currently working with around ninety users from thirteen different departments across Oxford University including, Biochemistry, Dunn School of Pathology, Chemistry, Physiology, Pharmacology, Plant Sciences, Earth Sciences, MRC Weatherall Institute of Molecular Medicine, Paediatrics, Wellcome Center of Human Genetics, Nuffifled Department of Clinical Neurosciences, Nuffield Department of Medicine and the Division of Structural Biology. We cover multidisciplinary exciting research projects from very diverse scientific areas in cellular and molecular biology to medicine and earth sciences.

How can someone book in to use the facility?

Visit the Advanced Proteomics Facility website

Please contact marjorie.fournier@bioch.ox.ac.uk for facility access and discussion of proteomics projects. We also provide quotation for grant applications.