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
EASY-nLC 1000 (UHPLC)
2012 Fully integrated nano-LC system designed to work at ultra high pressures up to 1000 bar.
- More Identifications
- High Resolution
- Fast Analysis Time 		LC-MS based Proteomics
Thermo Scientific

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

 

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