Agilent’s 6520 quadrupole time of flight mass spectrometer is a high-resolution instrument that can be used for various proteomic applications. The Q-TOF in our lab is interfaced with Agilent’s HPLC-chip cube system. HPLC chip integrates enrichment/trap column, analytical column, connection capillaries, and nanospray emitter directly on the polymer chip surface eliminating peak dispersion. We are using Q-TOF instrument for carrying out SILAC (http://www.silac.org/) and iTRAQ based quantitative proteomic profiling of gastrointestinal cancers to identify biomarkers and therapeutic targets. The instrument is also being used for several proteo-genomic efforts to annotate genomes.

LTQ Orbitrap Velos mass spectrometer is a hybrid Fourier Transform mass spectrometer that combines features of linear ion trap and orbitrap mass analyzer. This mass spectrometer has a unique dual-pressure linear ion trap that features a high-pressure cell for trapping, isolating and fragmenting precursor ions and a low pressure cell for scanning ions to the detectors for carrying out mass analysis. The instrument is also equipped with ETD (electron transfer dissociation) which is particularly useful for analyzing post-translational modifications like phosphorylation and glycosylation. We are using LTQ Orbitrap Velos for both qualitative and quantitative proteomics studies including characterization of post-translational modifications like phosphorylation, and glycosylation and identification of biomarkers of various neurological disorders.

The TSQ Quantum Ultra is a high performance triple stage quadrupole mass spectrometer featuring the Ion Max source with heated electrospray ionization probe and the Dual HyperQuad mass analyzers providing greater analytical selectivity. This mass spectrometer uses several different scan modes and enables constant neutral loss scanning, parent scanning, high-resolution precursor ion selectivity, Selected Reaction Monitoring (SRM), Highly Selective Reaction Monitoring (H-SRM) and Multiple Reaction Monitoring (MRM). We are using TSQ Quantum Ultra to validate disease biomarkers in serum, urine and other body fluids.

IOB houses an Agilent 1200 series HPLC system with a binary pump. This system is being used for offline fractionation of proteins and peptides for proteomic investigations. Further, we are using the LC system for serum depletion using multiple affinity removal system. Peptide level fractionation is largely being carried out using strong cation exchange chromatography.

 

IOB houses an Agilent 3100 OFFGEL Fractionator. This is an offline fractionation technique for protein and peptides based on isoelectric focusing technology. We are using this instrument for our proteomic investigations.