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 Lumos ETD
Tribrid linear ion trap-quadrupole-Orbitrap mass spectrometer. The tribrid architecture, with an independent ion-routing multipole which enables parallelization, significantly increases scan rates, and maximizes 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.
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 proteins
Liquid Chromatography
Ultimate 3000 RSLC System (Dionex)
Nano LC System - used for peptide separation interfaced directly to the Q-Exactive Plus for LC-MS/MS
Offline Sample Fractionation
1200 Infinity HPLC (Agilent) / Ultimate 3000 HPLC (ThermoFisher Scientific)
Offline analytical HPLC systems 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)
IsobarQuant (Franken H. et al. Nature Procotols, 2015)