TECHNOLOGIES


Mass Spectrometry

The Pandey lab is involved in developing proteomic methods as well in applying mass spectrometry for studying signaling pathways, identifying biomarkers and characterizing protein-protein interactions. The lab is equipped with a number of mass spectrometers including Agilent's 6538 Ultra High Definition Accurate-mass Q-TOF, Thermo's LTQ-Orbitrap XL ETD mass spectrometer and Agilent's 6430 Triple Quadrupole mass spectrometer.

Thermo LTQ Orbitrap Elite ETD mass spectrometer

The LTQ Orbitrap Elite is one of the Thermo hybrid Fourier Transform mass spectrometers that combines a linear ion trap mass analyzer with an Orbitrap mass analyzer. In addition to combination of fast scanning linear ion trap and high resolving power and mass accuracy of Orbitrap mass analyzer, this instrument has also equipped with ETD at the backend which allows the orthogonal, electron-based peptide/protein fragmentation, resulting in c/z fragment ions. The LTQ Orbitrap Elite ETD mass spectrometer has the highest resolving power (upto 480,000 of resolution at 400 m/z) with the proteomics grade scan speed. In addition to the conventional CID, the instrument also features an new, additional collision cell for higher energy collisional dissociation (HCD) which is much faster, as compared to any previous versions of HCD cells (e.g. XL and Velos). Maximizing almost all capabilities of previous Orbitrap-based mass spectrometers while providing higher sensitivity, resolution and mass accuracy makes it suitable for a variety of proteomics studies including PTMs analysis. We use the LTQ Orbitrap Elite mass spectrometer for mapping human proteome as a metaproteomics analysis.

Agilent's 6538 Ultra High Definition Accurate-mass Q-TOF

This mass spectrometer provides a very high resolution (40,000), high mass accuracy (parts per billion) and dynamic range (four to five orders of magnitude). The sensitivity of detection for peptides is in attomole range. The variable scan speed mode offers dynamic scan speed based on abundance of precursor peptides. Agilent's 6538 Q- TOF is interfaced with Agilent's HPLC chip-cube nanospray source which offers great advantage by reducing variation caused by manual intervention. In our laboratory, we are using this mass spectrometer for various proteomic applications such as proteogenomics, quantitative proteomics based on SILAC, iTRAQ, 18O labeling and label-free approaches and for the analysis of post-translational modification such as acetylation and phosphorylation.

Thermo LTQ Orbitrap XL mass spectrometer

Thermo LTQ Orbitrap XL mass spectrometer is a hybrid Fourier Transform mass spectrometer which combines features of linear ion trap and orbitrap mass analyzer. This combination of fast scanning linear ion trap and high resolving power and mass accuracy of orbitrap mass analyzer makes it one of the best mass spectrometers for proteomic research. The instrument also features an additional collision cell for higher energy collisional dissociation (HCD) which is particularly useful for analyzing ions in the low-mass region of the spectrum. Culminating almost all the capabilities of previous mass spectrometers while providing higher sensitivity, resolution and mass accuracy makes it suitable for a variety of proteomics studies. We use LTQ Orbitrap for both qualitative and quantitative proteomics studies including identification of biomarkers of GI cancers and characterization of post-translational modifications like phosphorylation and glycosylation.

Agilent's 6430 Triple Quadrupole LC/MS

This mass spectrometer is designed for true multiple reaction monitoring (MRM) based quantitation. The improved hexapole collision cell offers fast monitoring of multiple peptides with short dwell time enabling one to monitor hundreds to thousands of transitions in a single run. We are using this mass spectrometer to develop biomarker assays in serum, urine and tissues for developing MRM assays for early detection of cancers and other diseases.

3100 OFFGEL Fractionator

Agilent's 3100 OFFGEL fractionator can be used for in-solution pI based separation. Our lab utilizes this fractionation technique for fractionating proteins as well as peptides to obtain a deeper coverage of the proteome in a number of quantitative proteomics and proteogenomics projects.

HPLC Systems

Our lab has one 1200 series and three 1100 series HPLC systems from Agilent Technologies. We use these LC systems for both nano-flow and standard flow applications. In most projects, we carry out offline fractionation of proteins/peptides using various LC based techniques such as strong cation exchange chromatography (SCX), anion exchange chromatography and macroporous reversed phase chromatography. We also employ multiple affinity removal system for depletion of abundant proteins from serum, urine or other body fluids.