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Instruments present in our facility are:
SELDI-TOF-MS (surface enhanced laser desorption/ionisation-time of flight-mass spectrometer) This method uses proteinchip® arrays (Biorad) with different selective surfaces such as cation or anion exchange surfaces, hydrophobic surfaces and metal binding surfaces. Also antibodies, specific proteins and DNA can be bound to chips to study protein-protein and protein-DNA interactions. Cell lysate, plasma or urine is applied on the selective surface and, after washing, a subset of proteins is specifically bound. The chip is analyzed in a TOF-MS which generates a protein spectrum of the different molecular masses present on the proteinchip. This technology is suitable for research into molecular mechanisms of disease and biomarker identification. 
Fluorescence 2-D difference gel electrophoresis (DIGE) uses spectrally resolvable dyes to label protein samples prior to 2-D electrophoresis. By using different fluorescent dyes to separately label protein samples multiple samples can be co-separated and visualized on a single 2-D gel. This fluorescent multiplexing approach is compatible with mass spectrometry and overcomes many of the disadvantages of traditional 2-D analyses. A broad dynamic range provides more accurate quantitative data than traditional 2-D silver staining techniques while rapid image overlay simplifies image analysis and improves comparative accuracy.
This instrument is based on the SPR (Surface Plasmon Resonance) technology that enables real-time detection and monitoring of biomolecular binding events (e.g. protein-protein interactions). Biological processes are, for a large part, determined by protein-protein interactions which play a role in the pathogenesis of acquired or genetic diseases. Furthermore, protein-protein interactions, e.g. hormone-receptor interactions, are key targets for drug design. 
Surface Plasmon Resonance (SPR) technology: Upon binding of proteins a change in refractive index is measured which represents the change in molecular mass.
High-performance-liquid chromatography (HPLC) coupled to electrospray ionisation mass spectrometry (ESI-MS) is a powerful technique to separate peptides and proteins of lower molecular weight (appr. < 20 kDa). This technology will be further developed for large-scale analysis of biological fluids for new biomarkers of disease and other applications requiring high sample throughput.
Applied Biosystems Voyager DE Pro mass spectrometer with MALDI source Matrix Assisted Laser Desorption Ionization (MALDI) allows a quick and simple determination of the molecular weight of a protein, a peptide, and even mixtures of proteins and peptides. Combined with enzymatic digestion it will deliver a peptide mass fingerprint of a protein, wich can be used for searching a data base and identification of a protein. MALDI makes use of a matrix which absorbs the light of the laser puls that is fired on the sample. Sample ions are then liberated from the mixture of matrix and sample, and ions are detected by means of a time of flight mass spectrometer. The Voyager offers high sensitivity and high mass accuracy, and is simple to use in the work flow of a proteomics facility.
ABI-MDS/Sciex QSTAR hybrid mass spectrometer with ion sources for electrospray, nanospray, MALDI and SELDI The QSTAR is a versatile high-performance research mass spectrometer which comprises a quadrupole section for mass separation, a collision cell for ion fragmentation, and a Time-of -flight section for accurate mass determination. It can be combined with a nanobore HPLC system intended for the separation of peptide mixtures at high sensitivity. When the MALDI or SELDI sources are used, the ease of use of these ionization methods is combined with the extensive series of options for ion fragmentation and accurate mass measurement, aimed at the determination of the amino acid sequence of peptides and the structure elucidation of new biomarkers.
The Agilent 6510 Q-TOF LC/MS delivers a ten-fold sensitivity advantage, allowing the detection of critical, low-level components. At the same time, fast spectral acquisition allows the acquisition of higher-quality data and provides more information from complex samples. The system is equipped with the Agilent 1200 Series HPLC-Chip/MS system. This is a new microfluidic chip-based technology for nanospray LC/MS. Based on the HPLC-Chip and HPLC-Chip Cube MS interface, it provides a new level of nanospray MS sensitivity, robustness, ease of use and reliability.
HPLC-Chip Cube MS interface
LTQ Orbitrap high resolution MS The LTQ Orbitrap (Thermo Electron) can
deliver low-ppm mass accuracy
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