Equipment and software

Recent developments in mass spectrometry instrumentation have revolutionised the biochemists toolkit; allowing unprecedented protein expression profiling whilst at the same time allowing traditional assays akin to western blotting to be performed with unrivalled specificity using selected reaction monitoring assays.

Perhaps the most important impact of mass spectrometry is in the structural elucidation of post-translational modifications, an area in which no other technology comes close in terms of sensitivity, specificity and scale.

Our full range of euipment and software includes:

Mass spectrometry instruments

Thermo Orbitrap Elite

Thermo Orbitrap Elite

The Thermo Scientific Orbitrap Elite MS is a high performance hybrid mass spectrometer combining the novel high-field OrbitrapTM analyser with a dual-pressure linear ion trap, the Velos Pro, and is coupled online to a Dionex Ultimate 3000 uHPLC system for upstream separation of molecules of interest with an EASY-Spray™ Ion Source for ease of sample delivery and improved sensitivity through nanolitre flowrates.

Data acquisition and processing is handled through the powerful Xcalibur & Proteome Discoverer software suites. The VelosPro dual pressure ion trap combines high sensitivity, reliability, a high dynamic range with the ability to do MSn analysis.

The ultra-high resolution (>240,000 FWHM) of the novel high field orbitrap mass analyser provides certainty in analytical results by enabling molecular weight determination for intact proteins and in-depth analysis of isobaric species. The unsurpassed resolution of the system is especially useful when dealing with complex and low abundance samples.

The availability of multiple fragmentation techniques (Collision–induced dissociation, CID; High-energy Induced Collision-induced dissociation, HCD, Pulsed Q dissociation, PQD, and Electron Transfer Dissociation, ETD) offers a new level of versatility, sensitivity and performance for many research proteomic research applications including, but not limited to:

Through its high resolution and mass accuracy combined with high scan speeds our uHPLC-MSn using the Orbitrap Elite offers an excellent platform for studies in quantitative proteomics and PTM analysis, metabolomics / lipidomics, glycan identification / characterization as well as biopharmaceuticals (e.g. Intact antibody analysis) and pharmaceuticals (e.g. definitive metabolite identification).

ABSciex 4000 Qtrap

ABSciex 4000 QtrapThe ABSciex 4000 QTRAP® MS/MS System is a Hybrid Triple Quadrupole/Linear Ion trap mass spectrometer utilizing the powerful Analyst® and BioAnalyst® software, covering data acquisition and processing. Source ionization is through the reliable and flexible Turbo V™ ion source permitting both electrospray ionization (ESI) for LC-MS/MS, and atmospheric pressure chemical ionization (APCI), which is useful for non-readily ionisable compounds such as non-polar molecules. Also available is the NanoSpray® II ion source for nanolitre LC flowrates to improve sensitivity and useful in discreet nano-spray applications for limited sample amounts.

The QTRAP400, due to the adaptability of the triple quadrupole / trap layout permitting a wide range of scan types, useful for a wide range of discovery and quantitative assay applications such as:

  • Bottom-up proteomics is achieved through ABSciex’s Information Dependent Acquisition (IDA) software (part of Analyst®), which links high resolution survey scanning to high-sensitivity MS/MS scanning of the fragmentation ions for sensitive, fast and reliable peptide identification.
  • Post-translational modification discovery is achieved through the IDA software which links highly specific Precursor Ion (PI) and Neutral Loss (NL) scan functions to identify PTMs with high-sensitivity MS/MS scans to determine the modification sites.
  • Multiple-Reaction-Monitoring (MRM) is used for identification & quantification (relative or absolute) of small molecules such as peptides or pharmaceutical products and their metabolites, assisting in:
  • Biomarker discovery and validation.
  • Identification, quantification and characterization of metabolites.

Waters G2 Synapt

Waters G2 SynaptThe Waters G2 Synapt is a state of the art high performance ion mobility orthogonal mass spectrometer with nano-spray and MALDI. The provision of an ion mobility cell between the trap cell and the transfer cell before the TOF provide both an unparalleled resolution and an ability to do complex MS/MS interrogation of molecules. The ability to change the source rapidly make it an excellent machine for metabolite work where a large range of classes of organic molecules are involved. The ion mobility function brings a new dimension to MALDI-imaging experiments.

These parameters allow high resolution and high sensitivity for experiments involving:

  • Non-targeted metabolic profiling
  • MS/MS/MS analysis of ions for mass identification
  • Analysis of isomers
  • Nano-LC
  • MALDI-MS-imaging at single cell resolution
Sample preparation

Agilent OFFgel fractionator

OFFGEL fractionatorPre-fractionation of proteins and peptides prior to MS analysis may increase the number of proteins ultimately identified. biOMICS has the Agilent 3100 OFFGEL Fractionator which isoelectric focusing technique to achieve excellent pI-based fractionation as an alternative to HPLC fractionation. The resulting fractions are in solution, making recovery for MS analysis easier than with gel based methods.

Offline HPLC

Currently we have a Hewlett-Packard 1090 Series HPLC system that is available to be used for “offline” sample preparation, or analytical experimentation if so required. The 1090 series features a high quality HPLC pump (optimized pump performance at 50–5000 μl/min flow rates) auto-sampler, three solvent system (with supplied Helium for solvent degassing) with a heated column compartment, a diode array detector and a controlling Chemstation software equipped PC. Due to the wide choice in HPLC column chemistries, this provides a highly flexible platform in which to carry out fractionation (of varying resolution) of proteins/peptides prior to MS analysis.

Analight DPI

Dual Polarisation Interferometry (DPI) technology is a tag-less analytical technique with application in Surface Science and Biophysics. DPI uses polarised light from a laser passing down stacked waveguides. These waveguides are incorporated into the structure of the AnaChip™ range. Molecules, under study, are immobilised (physically or chemically) onto one of a range of AnaChip™ surfaces. The evanescent field emanating from the top waveguide interrogates the immobilised molecules. Changes in the resulting optical interference pattern are caused by changes in the structure and/or mass of the immobilised molecules. This permits measurement of the molecules mass, thickness and density at the surface of the AnaChip™.

See link for how the DPI technology works. The Analight permits a highly detailed analysis of protein interactions (amongst many other applications) to complement such MS analysis as interactome studies

Other equipment & software

Additional equipment

  • Sercon PDZ Europa 20-20 IRMS stable isotope analyser
  • Cryo-concentrator
  • Capillary electrophoresis
  • Gel electrophoresis


We have a wide range of instrument vendor software for mass spectrometry data analysis as well as a dedicated Mascot (Matrix science) server for peptide identification. Data analysis including spectral processing, peptide/protein identification and quantification is performed using Proteome Discoverer and MaxQuant.

All software is licensed for local use on a dedicated mirrored 20 terabyte server. We provide training and advice where appropriate on the use of software and interpretation of results.