Instrumentation

    Mass Spectrometry
  • The TripleTOF 5600+ system is a hybrid mass spectrometer that combines high performance quadrupole (Qq) mass spectrometry with high resolution Time-of-Flight (TOF) data acquisition and therefore provides a comprehensive platform for discovery and targeted proteomics as well as metabolomics and lipidomics. The wide mass range of the TOF-analyser (up to m/z 40,000) also facilitates intact protein mass measurements. The triple quadrupole-like performance in combination with the TOF-analyser enables us to run SWATH[[sitetree_link id=50]] (sequential window acquisition of all theoretical fragment ion spectra) protein profiling as well as high resolution MRM[[sitetree_link id=51]] (multiple reaction monitoring) assays as novel approaches in targeted quantitative proteomics (read more about SWATH[[sitetree_link id=50]] and high resolution MRM[[sitetree_link id=51]]). more »

  • The LTQ-Orbitrap is a hybrid mass spectrometer combining the strengths of two fundamentally different mass analysers. The front part is a robust very sensitive linear ion trap (dynamic electric field ion trap) mass spectrometer with high scan rates for high throughput analyses. The second mass analyser, the Orbitrap (static electric field ion trap), measures the m/z dependent frequency of a harmonic ion oscillation along a central electrode rode using non-destructive ion detection. more »

  • The MALDI tandem time-of-flight mass spectrometer combines the high mass accuracy and resolution of a TOF-analyser with highly specific precursor ion selection for sensitive CID (collision induced dissociation) analysis. Matrix assisted laser desorption/ionization is a robust ionisation method that tolerates certain amounts of additives/contaminations. The 4800 MALDI TOF/TOF-analyzer is able to separate molecules of a wide mass range. more »

  • Protein/peptide separation/fractionation
  • The Centre for Protein Research is equipped with different LC-systems suitable for the separation of peptides, proteins and various polar and non-polar compounds. We use a nanoflow/microflow Ultimate 3000 HPLC-instrument which is inline coupled to a Probot fraction collector for coupling RP-HPLC to MALDI tandem TOF-MS. Another Ultimate 3000 uHPLC system is inline coupled to the LTQ-Orbitrap MS. more »

  • We are performing small and large scale 2-D gel electrophoresis (IEF coupled with SDS-PAGE) for protein separation and quantification of relative protein abundances. 2-D PAGE is particularly suitable for differentially displaying the protein complements (up to ca. 1500 protein spots per sample) of two or more related samples such as disease vs healthy, time course experiments etc. more »

  • The 3100 OFFGEL Fractionator is used for the separation and fractionation of proteins and peptides by isoelectric focusing (IEF). The instrument can be used to (i) fractionate proteins and peptides prior to downstream analytical methods such as liquid chromatography coupled mass spectrometry (LC-MS), (ii) purify peptides, proteins or protein complexes and (iii) separate proteins by isoelectric focusing as the first dimension in classical 2-dimesnional gel electrophoresis. It can be operated in “off-gel” mode for an efficient in solution fractionation/separation or “in-gel” mode for conventional IEF. more »

  • Robotic workstations
  • In-gel enzymatic protein hydrolysis is the most crucial, and also the most labour intensive sample processing step for gel-based mass spectrometric protein identification. The liquid handling robotic workstation for protein digestion represents an efficient automation and standardisation of sample processing between gel electrophoretic protein separation and mass spectrometric protein identification. The automated protein digestion (i) allows a high sample throughput for large scale gel-based proteomics experiments, (ii) minimise hands-on work which avoids sample contamination that affects downstream mass spectrometry-based protein identification and (iii) standardise sample processing which gives more confidence for less experienced users. more »

  • The Probot workstation is a fraction collector that interfaces liquid chromatography with MALDI mass spectrometry. The Probot workstation is in-line coupled to nano-flow liquid chromatography. It automatically mixes the LC-fractions with matrix and spots them onto a MALDI plate. more »

  • Auxiliary Equipment
  • The CEM Discover Proteomics (Contributed by Gravida) is a system for temperature and power controlled microwave-assisted protein digestion. It allows for very short digestion periods of about 10 min. compared to the classical 16-24 h incubation time. more »

  • The Nanobaume Capillary Column Packing Bomb is used to fill and pack capillary columns of usually 50-100 µm inner diameter with different stationary phases. Typical stationary phases that we use for various nanoflow LC-applications are C4, C8, C18, HILIC, N2-HILIC, SCX. The bead size varies between 3 and 5 µm. more »