PROTEOMICS SERVICES AND COOPERATIONS
PROTEOMICS CORE FACILITY AT THE
EXPERIMENTAL OPHTHALMOLOGY
EXPERIMENTAL OPHTHALMOLOGY
The Experimental Ophthalmology has recently developed an advance mass spectrometry based Proteomics core unit.
Our facility can perform all standard proteomic procedures, mass spectrometry based profiling, and Protein microarrays.
We gained expertise in antibody and protein profiling using different technologies for more than 10 years. We could publish our results in ophthalmological and proteomic journals with the highest impact. We collaborate with some of the largest Europe-wide glaucoma studies: EGPS and GlaucoGENE group. The Experimental Ophthalmology in Mainz is the official Proteomics Center for both projects.
Our facility is open for collaborations and services to investigators from different institutes in and abroad. Please contact us for details.
Services Available
We can perform mass spectrometry based profiling using state of the art instruments. We use the Seldi-TOF Proteinchip technique (Biorad, USA). Furthermore, we can prefractionate complex samples using magnetic nanoparticles (e.g. Dynal and Bruker), which will be done with very high reproducibility by means of robotic stations (Tecan and Beckman robots). Then the samples with be measured by ultra high resolution Maldi-TOFTOF (Bruker, Ultraflex). This will be done in order to compare protein profiles from normals and diseased samples for purposes such as biomarker detection and identification (Clinical Proteomics).
For most sophisticated analysis, we built our own software pipeline, the PSP protein software project software, which will search for possible biomarkers using a combination of different algorithms such as artificial neural networks, multivariate statistics, and tree algorithms.
After tryptic digestion of spots excised from 1D or 2D gels, high-throughput protein identification (peptide mass fingerprinting) can be done by Bruker Ultraflex Maldi-TOFTOF. The data is sent to a MASCOT server search engine.
To analyze very complex samples, a prefractionation by means of LC prior to mass spectrometry can be beneficial. We can perform a prefractionation of complex samples by magnetic nanoparticles with different surfaces such as anionic exchanger followed by Nano-LC (liquid chromatography). This LC is directly coupled to a MALDI-spotter, which collects the chromatographic fractions directly onto the Maldi targets. The analysis will be performed in the Bruker Ultraflex Maldi-TOFTOF.
Our facility can spot customized protein microarrays using a specialized spotting system which is available within our unit. We use both antibody arrays for confirmation of protein biomarkers and antigen arrays in order to screen for autoimmune components due to changes in antibody profiles.
A very promising approach in comparison to the unselective prefractionation by different chromatographic surfaces is the use of immunoproteomics approaches. Samples are enriched by the binding to antibody which are bound to Protein-G beads. They are subsequently eluted and the mixture is profiles as described above.
Software Workflow for Proteomics Profiling studies:
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