The Core Facility for Mass Spectrometry focuses on the development, optimization and application of methods for quantitative proteome analysis. Our lab is equipped with four state-of-the-art mass spectrometry platforms including three timsTOF Pro platforms (Bruker Daltonik) and one Orbitrap Exploris 480 instruments with a FAIMS-Pro interface (Thermo Fisher Scientific). The mass spectrometers are coupled to UPLC systems (nanoElute, nanoAcquity, Ultimate 3000 RSLCnano and EvoSep One), which enable reproducible gradient configurations in the nanoflow and low microflow range.
Moreover, two offline high-performance liquid chromatography (HPLC) systems are available for protein purification, peptide fractionation and/or peptide enrichment (e.g. for phosphoproteomic workflows). We have established standardized sample preparation procedures for several applications, ranging from tissues to small amounts of starting materials. Our automated liquid handling robotic system allows the preparation of larger sample cohorts in a standardized fashion.
Our Core Facility services include proteomic sample preparation, data processing, bioinformatic analyses and statistical evaluation. We provide expert advice for our collaborators regarding the experimental design, sample handling and data interpretation as well as time requirements and other expenses for their individual projects. Please contact us in advance when planning an experiment.
Methods and workflows available:
- Protein identification: from tissues, cells and body fluids; from native and SDS gels
- Label-free quantitative proteome analysis: large-scale relative quantification of up to 8.000 proteins derived from small amounts of starting material (e.g. derived from tissues, cells, body fluids, including primary material)
- Label-based quantitative proteome analysis: SILAC-based approaches; isotop-labeled standard peptides (QConCAT) for absolute quantification
- Analysis of post-translational modifications: ubiquitination, phosporylations, others.
- Immunopeptidomics: isolation and label-free LC-MS/MS analysis of MHC-ligands
- Interactome analysis: identification of protein interaction partners after pulldown/immunoprecipitation experiments
- Cell secretome analysis: labelling and capture of newly synthesized, secreted proteins in cell culture followed by quantitative LC-MS analysis
- Other services: analysis of the protein N-terminome; characterization of nanoparticle coronas
- If you plan to perform any proteomic experiment or are interested in collaborating with the Core Facility for Mass Spectrometry, do not hesitate to contact us.