Applications

Small molecules/Metabolomics

Mass spectrometry can be used for the structure elucidation and quantification of small molecules, like metabolites. Since the chemical nature of the compounds to be analyzed varies over a wide range, we discuss each project with you to find the best suited experimental setup for each individual project.

Protein identification/Proteomics

Protein identification is a standard service of the core facility. We perform the tryptic digests of a gel-band or a sample in solution and analyze the resulting peptides with nanoHPLC-MS/MS. We have protocols established to deal with different types of samples even if they contain protease inhibitors or detergents. Though, you have to tell us if these compounds are present within your samples. The customer gets a database search report for each sample or depending on the type of analysis a comparative analysis. We use different bioinformatic software-packages to analyse the data, like PEAKS, Byonic, Proteome Discoverer, or MaxQuant and Perseus. In detail, following applications are available:

• Protein identification using gel/blot-bands or from solution
• Differential proteome studies (e.g. treated vs. untreated or    wild-type vs. mutant)
• Identification of binding partners and protein networks        using affinity proteomic methods (pull-downs, BioID, etc.).
  For pull-downs no elution of bound proteins is necessary. We have protocols established for digesting proteins “on-bead”.
• PTM-analysis for distinct target proteins or proteome-wide (phosphorylation, acetylation and ubiquitination are routinely available, other PTMs on request) Especially for complex projects like differential proteome studies we recommend to discuss the project with us in advance to find the best experimental setup and strategy. For most kinds of experiments it is highly recommended to use biological replicates. At least two, better three or four, which should be measured at the same time.

Mass determination of intact protein

We perform mass determinations of intact proteins using ESI-MS on the Synapt G2Si mass spectrometer. Routinely a mass accuracy of +/- 1 Da or 10 ppm, depending on the size of the proteins, is achieved. We are able to analyze proteins up to ~ 150 kDa, depending on the ionization efficiency of the proteins. If a native measurement is necessary (e.g. to measure non-covalent complexes or non-covalently bound inhibitors, substrates or co-factors), only low salt conditions like ammonium-acetate in concentrations up to 100 µM will be accepted.

Elemental analysis

Within the facility we also offer the quantitative analysis of trace elements. This is done with the ICP-MS (inductively coupled plasma mass spectrometry) or an MP-AES (atomic emission spectrometer).