Methods
and Services

The Translational Proteomics Core Facility offers state-of-the-art technologies for the automated high-throughput processing of clinical sample cohorts. We can process various sample types, including biofluids, e.g., blood plasma or cerebrospinal fluids, isolated cells, and tissue (both fresh and FFPE-fixed). Depending on your requirements, we use different sample preparation strategies and automated liquid handling systems to get the best possible results. Our state-of-the-art liquid chromatography systems ensure reproducible and sensitive peptide separation for high-throughput projects. The available mass spectrometers provide comprehensive proteomics datasets for relative and absolute quantification, fulfilling your scientific needs. All acquired data is stored on two independent petabyte storage servers for up to five years. With the 64-core workstation, hundreds to thousands of samples can be processed within days using powerful proteomics software tools. We provide basic data analyses and post-analytic consulting to enable you to answer your scientific questions.

The Protein Aggregation Capture (PAC) protocol can be used for various sample types. Specifically, it can process cells, tissues, and body fluids such as blood plasma and cerebrospinal fluid (CSF). Moreover, PAC is particularly well-suited for low sample volumes and samples containing detergents. We established an automated version of the protocol using the liquid handling platform Agilent AssayMap Bravo. By this, we can process up to 96 samples in parallel.
Additionally, the Agilent AssayMap Bravo liquid handling system can be used for the enrichment of posttranslational modifications, such as phosphorylated peptides.

Standard blood plasma studies suffer in proteomics depth because of the high dynamic range of the samples. Only a couple of proteins such as albumin make up major amounts of the total protein content in plasma samples. More interesting but low abundant proteins like inflammatory proteins are not detectable by classical strategies. Seer offers a proprietary, nanoparticle-based technology that enriches all proteins from blood plasma samples with similar affinities. While standard LC-MS analyses of plasma allow the detection of hundreds of samples the Seer Proteograph protocol enables the identification and quantification of thousands of proteins including protein isoforms.

We will combine the ultrasensitive and high-resolution Orbitrap Astral MS with the high-speed, high-precision Stellar MS in a single workflow. The high-resolution MS will be used for discovery measurements for the unbiased identification of new, potential protein biomarkers. After candidate selection, these candidates will be analyzed by targeted proteomics approaches for absolute quantification and validation of these candidates in a high throughput fashion. We envision faster progress in the validation of novel biomarkers and the associated preclinical benefits.

The Core Facilities thank the German Research Foundation for continuous support.