Facilities


   

Lab infrastructure

Equipment for mass-spectrometry-based proteomics

 

Module A. Gel flow

 

1. Gel-based protein separation (1D, 2D, native, blue native, BAC etc)
2. Fluorescent and non-fluorescent visualization of proteins
Instrument
Year
Features
General Applications
Company
Image
PowerScan
ViewPix 900
2009 -Scan Area
Transmitted light:
203 x 254mm 
Reflection:
216 x 297 mm
-Dynamic Range
65,536 gray levels (16 bit) 
281.5 E12 colors (48 bit)
- Resolution
Optical 4800dpi
Interpolated 12800 dpi
- control and archiving software argusX1 plus gray step wedge calibrated
Scanning acrylamide gels and other colorimetric labeled transparent samples  (suitable for wet gels) biostep

3. Image analysis using Delta2D
4. Spot/band marking and picking
5. Proteolytic Digestion
6. Sample lyphilization/concentration

Instrument
Year
Features
General Applications
Company
Image
Savant ISS110 2009 -Three drying rates
- Rotor RH64-11 for 64
1.5-2.0ml microcentrifuge tubes
- Rotor RD2MP for 2x96 shallow well microplates 
Speedvac Concentrator Thermo

Module B. Gel-free flow

      1. Liquid chromatography (nanoHPLC/FPLC) separation

      2. Preparative Isolectric Focusing

      1. Instrument
        Year
        Features
        General Applications
        Company
        Image
        3100 OFFgel Fractionator 2010 -Fractionation of up to 16 samples in parallel on two independent trays
        - High (24 fractions) or standard (12 fractions) resolution
        - Platform temperature
        10 oC – 35 oC
        - pI-based fractionation of proteins or peptides with liquid-phase recovery
        - conventional isoelectric focusing based on immobilized pH gradient gels
        Aggilent

      3. Proteolytic Digestion

      4. Sample lyophilization/concentration

      or

      1. Infusion of intact proteins


Module C. Liquid Chromatography-Mass spectrometry

Instrument
Year
Features
General Applications
Company
Image
EASY-nLC I 2009 Touch-screen control, Split-free design, fully integrated system

1 and 2D nano liquid chromatography

LC-MS -based Proteomics Thermo Scientific
Eksigent nanoLC400 2013 Split-free design 1 and 2D nano liquid chromatography  
Perkin-Elmer
HPLC
2013   liquid chromatography coupled to the Nexion ICP-MS Perkin-Elmer


Electro Spray Ionization-MS

Instrument Year Features General Applications Company Image
LTQ-Orbitrap XL with ETD 2009 Fragmentation Technology: CID, HCD, ETD
Mass Analyzers:
Linear Ion trap and Orbitrap

Electro Spray (Thremo)
nanoElectro Spray (Proxeon)

Proteomics, Phosphoproteomics, Label-free quantification, Intact protein analysis Thermo Scientific
Nexion ICP-MS 2013 Fragmentation Technology:
Mass Analyzers: 
Metallomics, Metaloproteomics,
Metal content of environmental samples Perkin-Elmer 
Perkin-Elmer

 

Module D. Bioinformatics analysis

    1. Xcalibur 2.0.7 (Thermo Scientific)

    2. Proteome Discoverer 1.3 (Thermo Scientific)

    3. Mascot server 2.3.01 (Matrix Sciences)

    4. Mascot Distiller 2.3.2 (Matrix Sciences)

    5. Mascot Daemon 2.3.0 (Matrix Sciences)

    6. Sieve 1.2 (Thermo Scientific)

    7. Peaks studio 4.5 (Bioinformatics Solutions - Thermo Scientific)

    8. Mass frontier 5.0 (HighChem Ltd - Thermo Scientific)

    9. ProMass 2.5 (Novatia - Thermo Scientific)

    10. Scaffold 3.0 (Proteome Software)

Computers and networking infrastructure