Proteomics Core FacilityInstrumentation and Software

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

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.   

QE_s

Q-Exactive (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).

HCT Ultra (Bruker)

3D ion trap mass spectrometer used for protein identification by LC-MS/MS  

 Q-Tof 2 (Waters)

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

QQQ_s

TSQ Vantage (Thermo Fisher)

Triple quadrupole mass spectrometer used for targeted quantification

MALDI micro MX (Waters)

MALDI Time-of-Flight mass spectrometer.  Used for protein identification by peptide mass fingerprinting (single proteins only)

Liquid Chromatography

TOP

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

Agilent_s

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 either High pH reverse phase or SCX mode.

Protein Separation and Imaging

2D Gel Equipment

Densitometer (GS-800, Bio-Rad)

Fluorescence imager (Molecular Imager FX, Bio-Rad)

UV Spectrometer (SmartSpec 3000, Bio-Rad)  

Software

Mascot (Matrix Science)

Proteome Discoverer (Thermo Fisher)

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

Peaks Studio (Bioinformatics Solutions Inc.)

Progenesis LC-MS (Nonlinear Dynamics Ltd)

Scaffold (Proteome Software)

Protein Lynx Global Server - PLGS (Waters)

ProteinScape (Bruker)