Center for Systems Biology and Molecular Medicine

Center for Systems Biology and Molecular Medicine

Instruments procured under BiSEP grant

Computational Infrastructure

  • Main workstation (HP Z840) reserved for NextGeneration-sequencing data analysis equiped with 2 X Intel Xeon E5-2699V4, 22C and 512GB RAM
  • Main workstation (HP Z840) reserved for proteomics data analysis equiped with Intel Xeon E5-2699V4, 22 cores and 128GB RAM
  • Sub workstations reserved for Genomics and proteomics data analysis (HP Z640) Intel Xeon E5-2683V4 2.1GHz 16C with 64GB RAM
  • NAS storege with 48TB storege space
  • Desktops with Intel Core i3, 4 GB RAM with 2TB HDD
  • Orbitrap Fusion Tribrid mass spectrometer

    Thermo Fisher Scientific Orbitrap Fusion Tribrid mass spectrometer is a tribrid Fourier Transform mass spectrometer that combines features of quadrupole mass filter, linear ion trap and orbitrap mass analyzer. This mass spectrometer provides ultra high resolution and enables precursor ion selection using a quadrupole mass filter and permits parallel analysis in both ion trap and Orbitrap mass analyzer thereby providing excellent sensitivity and selectivity. The instrument has multiple dissociation technique CID (collision induced dissociation), HCD (High energy C-Trap dissociation) and ETD (electron transfer dissociation), which provides flexibility of fragmentation and is particularly useful for analyzing post-translational modifications like phosphorylation and glycosylation. Automated Synchronous Precursor Selection (SPS) for MS3 significantly increases the number of peptides and proteins identified in high-complexity samples and improves quantitative accuracy when using isobaric mass tags. At YU-IOB CSBMM, we are using Orbitrap Fusion for both qualitative and quantitative proteomic studies including characterization of post-translational modifications and identification of biomarkers for various cancer and infectious diseases.

    Sciex QTRAP 6500 mass spectrometer

    At YU-IOB CSBMM Sciex QTRAP 6500 mass spectrometer with IonDrive technology provides ultra-high sensitivity, accuracy and precision at low concentrations. This mass spectrometer employs a combination of linear accelerator trap (LIT) and triple quadropole functionality with collision cell for effective MS/MS fragmentation and enables separation of isobaric species, isolate challenging co-eluting contaminants and reduce high background noise.One of the unique features of this mass spectrometer is its ability to carry out MRM3 analysis providing enhanced quantitative selectivity for peptide identification. The QTRAP 6500 mass spectrometer is coupled to Agilent 1290 Infinity II UHPLC system to provide exceptional separation capability. We are using this mass spectrometer to develop biomarker assays in serum, urine and saliva for developing MRM assays for early detection of cancers and infectious diseases.

    Hitachi Elite LACHROM HPLC system

    At YU-IOB CSBMM, we are using the HPLC system to carry out offline fractionation of proteins/peptides using various strategies such as strong cation exchange chromatography, anion exchange chromatography and reversed phase chromatography. We are also using the LC system for depletion of abundant proteins from body fluids using multiple affinity removal system. The HPLC system is coupled to a Gilson FC 203B fractionator which enables automated fraction collection.

    In addition to these high resolution mass spectrometry, YU-IOB CSBMM investigators have the access to various analytical, molecular biology, fungal and bacterial culture, animal cell culture facilities available at Yenepoya Research Center. Some of these instruments are listed below

    Thermo Scientific SAVANT LEGEND X1R Centrifuge

    Thermo Scientific SORVALLA LEGEND X1R Centrifuge

    Gel Doc system


    Inverted Microscope

    Millipore easyCyte

    BIO-RAD Cell Sorter

    PCI Ultrasonic

    Lab facilities