Dr Vinni Rajeeve
Mass Spectrometry Facility Manager

Professor Pedro R. Cutillas
Academic Advisor (proteomics) and Head of Facility

Dr Katiuscia Bianchi
Academic Advisor (flux analysis)

Mass Spectrometry

The CRUK Barts Centre Mass Spectrometry Facility provides proteomics and metabolomics flux analysis using Orbitrap instruments capable of high resolution and accurate mass measurements, and sample preparation methods. The service will support research projects by providing assistance with experimental design, sample preparation and data analysis. With improvements in technology in recent years, mass spectrometry has a myriad of applications in molecular and cellular biology including identification of compositions in protein complexes, label free quantitative proteomics, metabolic flux analysis, and post-translational modifications of proteins such as phosphorylation and acetylation.


The facility is equipped with LC-MS/MS systems based on different types of mass spectrometers serving different analytical purposes.

  • Q- Exactive Plus connected to an Ultimate 3000 nano LC - Untargeted proteomics and phosphoproteomics analysis
  • Q-Exactive connected to a Vanquish Quaternary UHPLC - Untargeted metabolic flux, and metabolomics analysis

The Mass Spectrometry Laboratory can provide access to advanced mass spectrometry, proteomics, metabolomics and flux analysis technologies.

There is a charge to cover mass spectrometry and reagent costs that the unit incurs to prepare and analyse samples.

Internal users: please visit the Intranet

QMUL users: please contact Dr Vinni Rajeeve

For external users: please contact Dr Vinni Rajeeve


A series of analytical techniques that enable:

  • Protein identification
  • Determination of protein post-translational modifications such as: phosphorylation, acetylation, and more
  • Relative quantification of proteins and their modifications
  • Absolute protein quantification in targeted mode
  • Molecular weight determination of intact proteins (top-down proteomics)

Metabolic flux and Metabolomics analysis

  • Metabolic flux analysis - Analysis of production and consumption rates of metabolites in a biological system using stable isotope labelled tracers
  • Metabolite identification/characterisation - Untargeted analysis or metabolic profiling of metabolites from biological fluids or tissues and targeted quantification of metabolites by LC-MS/MS

Sample preparation

The success of MS experiments is largely dependent on sample preparation. Many of the “off-the-shelf” biochemical methods commonly used to extract and analyse proteins and metabolites are not applicable to MS analyses, and thus sample preparation protocols. Therefore, it is strongly recommended that our experienced MS laboratory staff perform the critical steps of the relevant preparation procedures. Similarly, data analysis pipelines must be tailored to the particular application and research question and it is thus highly recommended to contract the laboratory in the early estates of experimental design.

Researchers submitting samples need to consult with MS staff regarding the initial steps of sample preparation.

Please contact us prior to starting your mass spectrometry analysis sample preparation.

Data analysis

  • Proteomics data are normally analysed by means of Mascot-driven database searches. Quantitative proteomics data are analysed using appropriate software depending on whether experiments are label-based or label-free. The results are provided in electronic format, including the protein hits, sequences of the corresponding peptides and, if applicable, the location of the modification sites and relative quantities.
  • Metabolomics and Metabolic Flux experiments should be tailored to the type of analytes of interest and data is analysed using the Thermo software family.
  • Targeted analysis of small molecules or proteins often requires optimisation of parent and fragment masses and chromatographic conditions.