“The Proteomics and Metabolomics Facility utilises advanced mass spectrometry techniques to improve our understanding of how proteins, their complexes and metabolites are regulated in health and disease.”

Modern mass spectrometry techniques allow the identification and quantification of proteins, their modifications and a range of metabolites from complex cellular systems. Facility users are encouraged to make contact at an early stage and involve facility staff in the planning and experimental design process.

The facility is equipped with three liquid chromatography-tandem mass spectrometry (LC-MS/MS) systems for proteomics analysis of a variety of sample types:

  • Thermo LTQ Orbitrap Velos
  • Thermo Q-Exactive
  • Thermo Q-Exactive HFX

Each of the mass spectrometers is coupled to a Dionex U3000 RSLC nanoflow chromatography system, which provides separation of complex peptide mixtures and enhances sensitivity in the analysis of limited sample amounts. Typical application areas are label-free quantification, analysis using stable isotope-labelled samples (such as SILAC), protein interaction studies, phospho-proteomics and the analysis of other post-translational modifications. We utilise multiple bioinformatics tools for data analysis and interpretation including MASCOT, MaxQuant and Progenesis QI as well as in-house developed R scripts. Further statistical analysis and data visualisation are enabled by the Perseus software platform.

For metabolite identification and quantification, we operate two LC-MS/MS and one gas chromatography-mass spectrometry (GC-MS) system:

  • Thermo Q-Exactive (coupled to Vanquish LC)
  • Waters TQ-XS (coupled to I-Class/M-Class UPLC)
  • Agilent 5977B MSD (coupled to 8890 GC)

This equipment supports targeted as well as untargeted metabolomics workflows and the most suitable approach depends on the respective biological questions. Metabolomics data analysis is equally supported by multiple software platforms, including MetaboAnalyst, Compound Discoverer, Progenesis QI and ProFIA.

We are also interested in exploring the spatial distribution of biomolecules within the context of multicellular tissues. In order to address this challenge we are interested in developing workflows for mass spectrometry imaging. To this end we are applying atmospheric pressure matrix-assisted laser desorption ionisation (AP-MALDI) with a SMALDI5-AF ion source (TransMIT GmbH) coupled to a Thermo Q-Exactive Plus mass spectrometer.

Selected Publications

Garcia-Luis J, Lazar-Stefanita L, Gutierrez-Escribano P, Thierry A, Cournac A, García A, González S, Sánchez M, Jarmuz A, Montoya A, Dore M, Kramer H, Karimi MM, Antequera F, Koszul R, Aragon L. (2019). FACT mediates cohesin function on chromatinNat Struct Mol Biol. 26(10): 970-979

Villoria MT, Gutiérrez-Escribano P, Alonso-Rodríguez E, Ramos F, Merino E, Campos A, Montoya A, Kramer H, Aragón L, Clemente-Blanco A. (2019). PP4 phosphatase cooperates in recombinational DNA repair by enhancing double-strand break end resectionNucleic Acids Res. 47(20): 10706–10727

Hudry B, de Goeij E, Mineo A, Gaspar P, Hadjieconomou D, Studd C, Mokochinski JB, Kramer HB, Plaçais PY, Preat T, Miguel-Aliaga I. (2019). Sex Differences in Intestinal Carbohydrate Metabolism Promote Food Intake and Sperm MaturationCell. 178(4), 901-918

Foster BM, Stolz P, Mulholland CB, Montoya A, Kramer H, Bultmann S, Bartke T. (2018). Critical Role of the UBL Domain in Stimulating the E3 Ubiquitin Ligase Activity of UHRF1 toward ChromatinMol Cell. 72(4), 739-752.e9

Madan B, Harmston N, Nallan G, Montoya A, Faull P, Petretto E, Virshup DM. (2018). Temporal dynamics of Wnt-dependent transcriptome reveal an oncogenic Wnt/MYC/ribosome axis. J Clin Invest. 128(12), 5620-5633

Millership SJ, Da Silva Xavier G, Choudhury AI, Bertazzo S, Chabosseau P, Pedroni SM, Irvine EE, Montoya A, Faull P, Taylor WR, Kerr-Conte J, Pattou F, Ferrer J, Christian M, John RM, Latreille M, Liu M, Rutter GA, Scott J, Withers DJ. (2018). Neuronatin regulates pancreatic β cell insulin content and secretion. J Clin Invest. 128(8), 3369-3381

Link J, Paouneskou D, Velkova M, Daryabeigi A, Laos T, Labella S, Barroso C, Pacheco Piñol S, Montoya A, Kramer H, Woglar A, Baudrimont A, Markert SM, Stigloher C, Martinez-Perez E, Dammermann A, Alsheimer M, Zetka M, Jantsch V. (2018). Transient and Partial Nuclear Lamina Disruption Promotes Chromosome Movement in Early Meiotic Prophase. Dev Cell.  45(2), 212-225.e7