Proteomics Platform

The GQ Proteomics Platform currently operates four mass spectrometers, with a combined capacity of over 400 samples per week. Two LC-QToF micro™ (Waters) each provide sensitive and reliable tandem MS/MS data for subsequent identification of peptides and proteins from complex mixtures using Mascot (Matrix Science). Alternately, samples can be analyzed on a MALDI-QToF Ultima™ mass spectrometer (Waters). This is a high accuracy, high-throughput machine ideally suited for samples derived from 2D gels and provides both peptide mass and sequence tag information.

The Platform also offers access to a 4000 Q Trap® (Applied Biosystems/MDS Sciex). The QTrap 4000 LC/MS/MS system is a high-performance hybrid triple quadrupole/linear ion trap mass spectrometer that enables high-sensitivity full-scan MS, MS/MS, and MS3 with high-selectivity from true triple quadrupole precursor ion (PI) and neutral loss (NL) scans. In addition to providing additional capacity for protein identification by LC-tandem MS, this instrument allows the operator to perform multiple reaction monitoring (MRM) for quantitation using the highest sensitivity triple quadrupole available and to identify and sequence post-translationally modified (PTM) peptides automatically in a single LC/MS/MS run.

As an alternative to gel electrophoresis and in-gel digestion followed by mass spectrometry, researchers now have the option to directly digest samples such as immunoprecipitates or recombinant proteins in solution.  Proteins are digested in solution with trypsin and the resulting peptides are separated by either 1D or 2D-LC prior to injection on the mass spectrometer. The Platform currently performs online 2D-LC separation using a strong cation exchange (SCX) column connected in series with a reversed-phase (RP) column on an Agilent 1100 Nanoflow LC system attached to a 4000 Q Trap® or to a LC-QToF micro™ mass spectrometer. Tryptic peptides are loaded onto the SCX column, washed and eluted stepwise by injecting salt plugs of increasing ionic strength. In the second dimension, these peptides are trapped on a RP enrichment column and separated by analytical RP-HPLC. This approach is capable of resolving many proteins in complex mixtures.