The Proteomics Core Facility maintains and uses equipment for protein separation and imaging, as well as for sample preparation for mass spectrometry.  We are equipped with state-of-the-art chromatography systems and mass spectrometers for LC, MS and LC-MS/MS, with a wide range of bioinformatic tools for data interpretation and evaluation. 

Mass Spectrometry

Orbitrap Fusion ETD

Tribrid linear ion trap-quadrupole-Orbitrap mass spectrometer. The tribrid architecture, with an independent ion-routing multipole which enables parallelisation, significantly increases scan rates, and maximises versatility. Any of three dissociation techniques — CID, HCD, and ETD — can be performed at any fragmentation stage, followed by analysis in either the linear ion trap or Orbitrap mass analyzer.

LTQ Orbitrap Velos Pro (Thermo Fisher)

Hybrid linear ion trap-Orbitrap mass spectrometer.  Used for protein identification and quantification by LC-MS/MS.  Principally used for complex samples and identification of post-translational modifications.  Both CID (low resolution) and HCD (high resolution) options available for MS/MS fragmentation.   

Q-Exactive Plus (Thermo Fisher)

Hybrid quadrupole-Orbitrap mass spectrometer.  Used for protein identification and quantification by LC-MS/MS. Principally used for complex samples and identification of post-translational modifications. HCD (high resolution) fragmentation allows for use of MS2 quantification strategies (eg. TMT labelling).

Q-Tof Premier (Waters)

Quadrupole Time-of-Flight electrospray mass spectrometer. Used in combination with HPLC (C4 column) for mass determination of intact protein

TSQ Vantage (Thermo Fisher)

Triple quadrupole mass spectrometer used for targeted quantification

Liquid Chromatography

NanoAcquity UPLC System (Waters)

Nano LC System — used for peptide separation interfaced directly to the Orbitraps and Triple Quad for LC-MS/MS

Ultimate 3000 RSLC System (Dionex)

Nano LC System — used for peptide separation interfaced directly to the ion traps and the Q-Exactive for LC-MS/MS

Offline Sample Fractionation

1200 Infinity HPLC (Agilent)

Offline analytical HPLC system with quarternary pumps, variable wavelength UV detector and micro fraction collector. For pre-fractionation of complex protein digests prior to LC-MS/MS. Operates in High pH reverse phase mode.

Protein Separation and Imaging

SDS PAGE equipment

Calibrated Densitometer (GS-900, Bio-Rad)

Software

Mascot (Matrix Science)

Proteome Discoverer (Thermo Fisher)

MaxQuant (Max Planck Institute of Biochemistry, Martinsried, Germany)

Scaffold (Proteome Software)

ProteinScape (Bruker)

IsobarQuant (Franken H. et al. Nature Procotols, 2015)