Hardware
The Analytics Core Facility Essen harbors a number of state-of-the-art mass spectrometers, liquid chromatography systems and other equipment needed for proteomics and analysis of small molecules (all located in our rooms/labs). If you are interested to use one of our services or if you want to discuss the feasibility and implementation of one of your ideas, please contact us. We will help to find customized solutions for your research needs.
Orbitrap Fusion Lumos (with ETD)
The Orbitrap Fusion Lumos (Thermo Scientific) is a Tribrid mass spectrometry system. It combines three mass analyzers (quadrupole, ion trap and high-field Orbitrap) that work together and in parallel which makes the system ideal for the analysis of proteomics and metabolomics samples. The complex analytes (e.g. peptides from tryptic digests, enriched metabolites etc.) are separated by ultra high pressure liquid chromatography (UHPLC) using the split-free nano-flow Easy-nLC 1200 (Thermo Scientific) and are directly fed to the MS via the Nanospray Flex Ion Source.
The Fusion is also equipped with a HDx-PAL robot for the on-line preparation of hydrogen-deuterium exchange samples and an Ultimate NCP-3500RS pump.
Orbitrap Fusion Lumos (right) with Easy nLC 1200 (middle) and HDx PAL (left).
Orbitrap Elite (with ETD)
The Orbitrap Elite (Thermo Scientific) is a hybrid mass spectrometry system. It combines the Velos Pro ion trap with the high-field Orbitrap and the ETD (Electron Transfer Dissociation) unit. The system is particularly suited for the analysis of proteomics and metabolomics samples. The complex analytes (e.g. peptides from tryptic digests, enriched metabolites etc.) are separated by ultra high pressure liquid chromatography (UHPLC) using the split-free nano-flow Easy-nLC 1000 (Thermo Scientific) and are directly fed to the MS via the Nanospray Flex Ion Source.
Orbitrap Elite (right) and Easy nLC 1000 (left).
Exactive Plus EMR with nanoMate
The Exactive Plus EMR mass spectrometer (Thermo Scientific) is a further development of the Exactive mass spectrometer and features a classic Orbitrap. With its extended mass range of m/z 20000, this machine can reliably determine the mass of complexes up to 2 MDa (2×106 Da). Protein samples in their native state are supplied to the mass spectrometer either via direct infusion (borosilicate emitters with conductive coating hooked up to the Nano ES ion source head of the Nanospray Flex ion source) or using the Advion Traiversa nanoMate.
Exactive PLUS EMR connected to the Advion Triversa Nanomate (dark blue).
LCQ Fleet with Ultimate 3000
The LCQ Fleet (Thermo Scientific) is low resolution mass spectrometry system for the analysis of small molecules and is typically used for reaction control during chemical synthesis. The complex compound/reaction mixture are chromatographically separated using an attached Ultimate 3000 HPLC.
LCQ Fleet (right) with connected Ultimate 3000 (Left).
Evosep One
The Evosep One is our latest LC acquisition and is primarily used for the analysis of low complexity or clinical samples. The Evosep One is in many ways different from classical LC’s. While in classical LC’s the sample has to be first loaded on a trap column or directly onto the analytical column sample loading in the case of the Evosep One is done off-line onto Evotips (disposable trap columns). The analytes are then automatically washed off the Evotip and into the Evosep One. Here the samples are diluted resulting in a pre-formed gradient. The whole gradient with the analytes is then transferred into a sample loop and sent over the analytical column using one high pressure pump. The pre formed gradients cannot be modified and require special columns (this is the biggest disadvantage of the Evosep One). However, the standardized platform allows the high throughput analysis of 15 - 300 samples per day (depending on the gradient and column used). The combination of high throughput (up to 300 SPD) with disposable trap columns (massive reduction of carry over) makes the Evosep One very attractive for the analysis of clinical samples and marker identification.
"Evosep One: Gradient off-set focusing UHPLC instrument for robust and high throughput proteomics”.
Typhoon FLA 9000
The Typhoon FLA 9000 Scanner is a versatile laser scanner for biomolecular imaging applications. We use it primarily for in-gel visualization of protein targets of fluorescent small molecules (activity-based protein profiling). It can, however, also be used in many other applications. For example, it allows sensitive and quantitative measurements of radioisotopic labels by storage phosphor, analysis of chemifluorescent Western blots, and multiplex fluorescence (e.g. DIGE applications, Western blotting with fluorescent antibodies).
Typhoon FLA9000
Electrophoresis Equipment
The analytics core facility is furnished with a variety of different state-of-the-art electrophoresis machines. We are able to run 1D samples in mini (8x10 cm), midi (13x22-28cm) and also in a high-throughput manner on maxi gels (40 x 16 cm). We are also well equipped to perform all kinds of 2D experiments (Ettan IPGphor 3 for isoelectric focusing; Ettan Dalt6 for parallel electrophoresis of up to 6 20x20 gels).
Gel chambers (from left to right mini, midi, maxi).
Ettan Dalt6
IPGphor3
Computing Hardware
We are running a dedicated Dell server (2 Intel Xeon 6 core Processors, 64 Gb RAM, 1.5 Tb HDD) on which we perform Mascot and MaxQuant searches. Additionally, we have MaxQuant running on two virtual machines (VM) via the VDI environment of the Faculty of Biology and the CViS (Competence Cluster for Virtual Systems) (accessible via VMWare Horizon View). The dedicated VM1 emulates 32 cores (Xeon v4 with 3.0 GHz) and 64 GB RAM while dedicated VM2 emulates 36 cores (Xeon Gold 6514 with 3.0 GHz) and 152 GB RAM. Both VM’s are operated in a server cluster with currently 6 nodes which guarantees maximum availability and a highly flexible accessibility (independent of time/place and computing platform).