RESEARCH SERVICES AND SUPPORT ACTIVITIES

List of services offered to users:

• Mass Spectrometry
  • Protein Identification by MS
  • Protein Quantitation by MS (in perspective also through SILAC e ICAT)
  • Metabolic profiles LC-M
  • Biomarker discovery
  • Post Translational Modification
  • Molecular characterization
  • Quantitative SRM / MRM analyzes
  • MALDI-MS Analysis
• Gel Based Proteomics
  • Preparation of samples for mass spectrometric analysis
  • One-dimensional electrophoresis (1D electrophoresis)
  • Two-dimensional electrophoresis (2D electrophoresis)
  • Painting and quantitative analysis of 1D and 2D gels with dedicated programs
  • Differential proteomics
  • Phosphoproteomics
  • 2D non-reducing / reducing electrophoresis
  • Training on proteomics techniques
  • Experimentation assistance to define the most appropriate experimental design to answer the biological question of interest
• Bioinformatics
  • Computational Mass Spectrometry. Management and analysis of mass spectra, including their pre-processing and extraction of significant signals, through open source and self-developed software. Preparation and submission of data on raw data repository.
  • Visualization and analysis of molecular interactions and related networks. Analysis of molecular interactions through CytoScape starting from databases of molecular interactions and metabolic pathways.
  • Preparation of databases and websites. Setting up on the Institute’s virtual server of databases and websites for the management and analysis of data for research, in particular in relation to proteomics and mass spectrometry.
• Three-dimensional models of biological macromolecules, docking simulations and drug design
  • Determination of the three-dimensional structure of biological macromolecules by analyzing X-ray diffraction data from crystals. The measurements will be carried out at the ESRF (Grenoble – F), ELETTRA (Trieste – I) and Diamond (Oxford – UK) synchrotrons to which access is guaranteed
  • Construction and refinement of three-dimensional models of biomolecules determined experimentally or “in silico”
  • Rational drug design based on the knowledge of the atomic structure of biological targets
  • Molecular docking simulations between protein and ligand, protein: protein, Protein: DNA
• Molecular Modeling and Molecular Dynamics
  • Validation of molecular models by comparing both hydrodynamic and SAXS experimental data with those calculated starting from atomic structures
  • Molecular dynamics simulations of complex biological systems (Proteins / DNA) through classical computational chemistry simulations (GROMACS)
• Biochemical-structural characterization of proteins and other biopolymers
  • Hydrodynamic radius in solution via DLS
  • Presentation of beamtime requests to perform HPLC-SAXS measurements at synchrotrons (preferential access to the SOLEIl synchrotron, Gif-sur-Yvette, FR)
• Cell and molecular biology
  • Cloning, expression and purification of recombinant proteins in prokaryotic cells
  • Tandem Affinity Purification
  • MTT Assay
  • Transient and stable transfections in human cell lines
  • Studies on transcriptional and post-transcriptonal regulation of gene expression by microRNAs by luciferase-based reporter assays
  • Studies on post-translational regulation of gene expression by fluorescence-based  assays
  • Evaluation of autophagy, ubiquitin-proteasome function, inflammatory pathways by fluorescence-based  assays

TOOLS AVAILABLE AT THE UOS PROTEOMICS AND MASS SPECTOMETRY

• • UltraFextreme MALDI-TOF/TOF mass spectrometer for MALDI imaging
  • Beckman DU640 UV-Vis spectrophotometer, thermostated and with motorized six-position cuvette holder.
  • Jasco V-530 UV-Vis spectrophotometer
  • Spot-picker BioRad The Protein Works
  • BioRad GS-800 Calibrated Densitometer
  • BioRad Pharos FX Molecular Imager
  • Beckman TL-100 Tabletop Ultracentrifuge with fixed angle rotor and swinging-buckets rotor
  • Perkin-Elmer 200 series HPLC system equipped with dual pump, autosampler, UV-Vis detector, Waters 474 Scanning Fluorescent detector, Wyatt DAWN DSP-F multi-angle light scattering (MALS) detector (obsolete), Wyatt Optilab DSP Interferential Refractometer .
  • Agilent 1200 series two-dimensional HPLC system equipped with two capillary pumps, standard flow pump, DAD UV-Vis detector, two thermostatted column compartments equipped with 6 and 10 position valves, capillary flow autosampler, standard flow autosampler, fraction collector, two degassers.
  • Agilent 6210 Series High Resolution Time-of-Flight Mass Spectrometer, equipped with ESI source and AP-MALDI (currently awaiting repair).
  • TECAN Freedom Evo robotic liquid handling system (jointly owned with Molecular Pathology).
  • Thermo Fisher Q Exactive Plus high resolution mass spectrometer with ESI interface and nano ESI equipped with any AP-MALDI source.
  • Thermo Fisher “Vanquish” HPLC system equipped with binary pump, column compartment autosampler.
  • Thermo Fisher “Ultimate Nano RSLC” UHPLC chromatography system, equipped with binary gradient pump, autosampler, variable wavelength detector.
  • One dimensional polyacrylamide gel electrophoresis equipment
  • Equipment for high resolution two-dimensional polyacrylamide gel electrophoresis with the use of real estate
  • Complete equipment for Western blotting and Southern – Western blotting of polyacrylamide gels
  • Beckman GS-6R refrigerated benchtop centrifuge
  • Eppendorf mini-spin centrifuge
  • OPTIMA Beckman Ultracentrifuge No. inv. 26418
  • Cryostat Leitz 1720
  • Liquid nitrogen containers for cryopreservation of cells and biological material
  • Virtual server made available by IRCCS Policlinico San Martino. Configuration based on quad core AMD Opteron 4171 HE, 64 bit, 2 GHz CPU with 7 Gb RAM. Ubuntu Server 14.04.5 LTS operating system. Apache, PHP and MySQL versions updated based on Ubuntu distribution.
  • Virtual server made available by GARR. Current configuration based on quad core Intel Xeon E3, 64 bit, 2 GHz CPU with 8 Gb RAM, expanding. Ubuntu Server 16.04.5 LTS operating system. Apache, PHP and MySQL versions updated based on Ubuntu distribution.
  • Software for the identification of proteins “Proteome Discoverer”.
  • “Compound Discoverer” software for metabolomics studies.
  • Two CO2 incubators for cell culture New Brunswick S170
  • Millipore Direct Q-5 UV ultra pure water (type 1) production system with 30 liter tank