The Mass Spectrometry and Proteomic Core Facility is make cutting edge mass spectrometry technology available to RGCB researchers as well as the wider academic and life science industry community While being a core facility, a major goal of the facility is to become a research environment for multidisciplinary research that utilizes mass spectrometry and other proteomics technologies to understand the disease biology and molecular medicine in the post-genomic era.

Infrastructure: RGCB Proteomics Core Facility houses the following instrumentation

Synapt G2-HDMS from Waters

This is a hybrid Quadrupole-Time of Flight (Q-TOF) mass spectrometer with an extra feature called Ion-Mobility by which compounds can be further separated and resolved based on their shape. The SYNAPT G2 system features new QuanTof technology that combines an innovative high field pusher and dual stage reflectron with a novel ion detection system in an optimised, folded, TOF geometry. Together these features provide a new dimension of high resolution, exact mass and quantitative performance uniquely available at acquisition rates that are compatible with UPLC separations.

NanoAcquity UPLCs from Waters

Proteomic core has one nanoACQUITY UltraPerformance LC® (UPLC® ) System and another nanoACQUITY UPLC® System with 2D Technology. NanoAcquity UPLC is designed for nano-scale, capillary, and narrow-bore separations to attain the highest chromatographic resolution, sensitivity, and reproducibility.

The nanoACQUITY UPLC® System with 2D Technology expands the use of sub-2-micron particles to achieve high peak capacity separations. This innovative system effectively uses two-dimensional (2D) UPLC for better chromatographic resolution of complex proteomic samples by using a dual reversed-phase (RP) approach.

Hydrogen Deuterium Exchanger (HDX) from Waters

HDX by mass spectrometry opens new windows into the dynamics of biomolecules by providing information on the relative deuterium uptake of different conformations of a protein, or locations within a protein. The nanoACQUITY UPLC™ System with HDX Technology leverages UPLC® separations and high-resolution MS to answer important questions about changes in protein conformation including: drug binding to a protein, protein-protein interactions, and protein folding.

UltrafleXtreme MALDI-TOF/TOF from Bruker Daltonik

This Mass spectrometer combines a MALDI source with a TOF/TOF tandem mass analyzer to acquire both high resolution peptide mass fingerprint data and MS/MS spectra of peptide ions. This MALDI-TOF/TOF Combines true 2 kHz speed in TOF mode and 1 kHz in TOF/TOF mode with ultrahigh performance and extreme flexibility for a broad variety of proteomics applications. In addition, the smartbeam-II™ laser enables ultra-high data acquisition speed in both MS and MS/MS at full systems performance

EASY-nLC II from Bruker

The EASY-nLC II is a nano-flow HPLC system tailored to the requirements proteomics applications. This LC system is used to separate protein and peptide mixtures for MALDI MS. The system is used in combination with a MALDI spotter.

Proteineer fcII from Bruker

Proteineer fc II is a MALDI spotter which enables automatic liquid handling for MALDI preparation of LC separated peptide fractions. It is designed to deposit fractions eluting from a NanoLC column (Easy-nLC II ) onto a MALDI plate, with the MALDI matrix automatically being added for offline MS and MS/MS analysis.

MALDI Tissue Imaging Setup from Bruker

It is a device for MALDI imaging sample preparation based on vibrational vaporization of matrix solution.

Off-Gel Liquid Phase IEF system from Agilent

This Agilent 3100 OFFGEL Fractionator uses a novel isoelectric focusing technique to achieve excellent Isoelectric point (pI)-based fractionation. The resulting fractions are in solution, making recovery for LC/MS analysis much easier.

ProteOn™ XPR36 Surface Plasmon Resonance (SPR) System (Bio-Rad)

The ProteOn™ XPR36 protein interaction array system monitors in a label-free manner the interaction of biomolecules in real-time using surface plasmon resonance (SPR) technology. Interactions are monitored over time by detecting the binding of an analyte flowing in a microfluidic channel to a ligand immobilized on a sensor chip. This system generates a 6 x 6 interaction array for the simultaneous analysis of up to six ligands with up to six analytes.

Experion Microfluidic base-on-Chip Electrophoresis System (Biorad)

This automated platform for nucleic acid and protein analysis incorporates LabChip technology into an integrated system that performs multiple electrophoresis steps in one. It automatically performs all the steps of gel-based electrophoresis (sample separation, staining, destaining, imaging, band detection, and even some data analysis) to deliver reproducible separation and quantitation results in just 30 minutes. Software analysis tools are offered for flexible data analysis.

The Proteomic Core will create a sample preparation laboratory to support scientists in processing their samples before the mass spectrometry analysis. The facility will also maintain an independent workstation dedicated for Mascot server, and 2 separate data stations dedicated for proteomics data processing.

Services

The Core will provide to both internal and external users at a service cost, high-sensitivity and high-resolution mass spectrometry analysis for protein and peptide characterization as its primary technology. The services offered will be:

  • Basic mass analysis of peptides and proteins: using MALDI-TOF/TOF and/or Waters LC/MS/MS (Q-TOF)
  • Protein identification with MSMS sequencing: Analysis could be done by using MALDI-TOF/TOF and/or Waters LC/MS/MS (Q-TOF). Protein identifications are made using state-of-the-art database search engines running on dedicated servers, with the capability of searching standard or custom protein databases.
  • Post translational modification analysis: The ETD capability of Waters Synapt G2 HDMS is an extremely powerful tool for identifying and characterising post-translational modifications, as well as the precise site within a protein where the modification occurs.
  • Protein relative quantitation: Protein quantitation can be accomplished using a 'gel free, label-free' technology which provides both relative quantitation (test vs. control). Alternatively, isotope-coded (labeled) samples can be analyzed to provide relative quantitation information. The analysis will be done on Waters LC/MS/MS system.
  • Protein-Protein Interaction Analysis: Protein interaction analysis will be performed by using BioRad ProteonXPR system and Waters NanoUPLC coupled HDX manager.

Proteomics Core Facility @ Campus 3

The Proteomics Core Facility (PCF) offers LC-MS/MS analysis, including a broad range of services, from mass confirmations to large-scale quantitative proteomic screens, along with all the associated bioinformatics, for clients on and off camps.

Mass spectrometry instrumentation available:

AB SCIEX 3200 QTRAP® LC/MS/MS System

The hybrid quadrupole/linear ion trap technology of the 3200 QTRAP® System provides the ability to identify and quantitate components from complex samples in a single run. Triple quadrupole specificity and quantitation combine with ion trap full-scan MS/MS sensitivity for simultaneous qualitative and quantitative results.

For further help & support contact us at +91-471-2529540 (Dr. Abdul Jaleel K. A)