Proteomics Core Facility Cologne

Deep proteome profiling

To obtain best possible coverage and penetration of a complete proteome we perform offline peptide fractionation by basic reversed phase chromatography. This enables the routine identification of proteomes to a depth of up to 10,000 proteins.

Secretome analysis

Highly specific enrichment of secreted proteins via click chemistry facilitates the direct quantification of differentially secreted proteins against the background of serum proteins in cell culture medium. 

Global proteome quantification

We use single shot analysis in DDA or DIA mode to profile changes in protein abundance between different groups of samples. Quantification of several thousands of proteins is easily achieved from any type of sample.

Targeted assays

Accurate quantification of a defined set of sentinel proteins among a large cohort of samples can be achieved by targeted assays (PRM), selectively detecting only the peptides of interest with high sensitivity.

Protein turnover

Metabolic pulse labeling with stable isotope-coded amino acids (SILAC) enables deciphering of protein synthesis and turnover rates in most cell culture systems and even mice.

Ultrasensitive sample preparation

We have implemented next-generation sample preparation technology (SP3) for samples containing just minute amount of protein down to the sub-µg range. SP3 is the method of choice for samples derived from FACS or laser capture microdissection.

Plasma profiling

We use data-independent acquisition approaches (DIA or SWATH) for robust quantification of proteins from plasma. As little as 5 µL non-depleted plasma is more than sufficient to profile on average >300 proteins over large sets of clinical samples.

Post-translational modifications

PTMs are key determinants in cellular signaling. We provide solutions for global screening of modified residues following peptide enrichment, including but not limited to phosphorylation, acetylation, and ubiquitination. 

Complexome profiling

The identification of novel protein complex members is facilitated by complexome profiling. Using blue native-PAGE or size exclusion chromatography (SEC), we can fractionate native protein complexes and use a correlation approach to unravel novel members of cellular protein assemblies.

Antibody validation

You have an antibody that works nicely for imaging or western blot, but it‘s performance for use in Co-IP is unknown? We can help you validate the antibody in terms of specificity and off-target binding, or to check how it performs under modified buffer conditions.

Spatial organization of protein interactions

Protein-protein interactions depend on the subcellular localization. We support approaches using enzymatic tagging by fusion proteins (e.g. APEX or BioID), to specifically enrich and identify binding partners of proteins from defined subcellular compartments.

Affinity purification-ms

Identification of interaction partners of a protein of interest is a routine application in our lab. We can work with virtually any kind of affinity handle and AP buffer compositions.

Protein id from cut gel bands

The identification of an unknown or unexpected band from SDS-PAGE gels is straightforward. We try to help you find out which protein it is, if it is modified or if part of the sequence has been cleaved.

Data dissemination for publications

Nowadays most journals require that the raw data of proteomic experiments are made publicly available. We take care of that on your behalf and make sure that the data will be online in the correct format directly after publication.


We operate a 80-core workstation dedicated for raw data processing. Basic statistical analysis is included for all projects. More advanced analyses (multivariate statistics, time-course analysis, multi-OMICS integration) can be included for more complex projects.

Scientific consultation

You are working on a grant application for a project that includes proteomic experiments? We are happy to assist you with the experimental design, cost estimation, or just with proofreading of your proposal.

Single protein characterization

You are studying just a single protein? We can employ a number of tools to analyze it in great detail, e.g. intact protein mass determination to find unknown modifications or multi-protease mapping for maximal sequence coverage.

How can we help you?

Looking for something else? Get in touch with us to discuss how we can support you with your specific challenge!