Research Group ‘Bioanalytics’
Prof. Dr. Henning Urlaub
Our group focuses on the development and application of mass spectrometry-based methods for proteome analysis. Located in the Institute of Clinical Chemistry, it encompasses the UMG’s Core Facility Proteomics led by Christof Lenz, and is associated to Henning Urlaub’s research group ‘Bioanalytical Mass Spectrometry’ at the Max Planck Institute for Biophysical Chemistry, Göttingen via a bridge professorship.
Protein-protein cross-linking mass spectrometry (XL-MS) for the analysis of protein-protein interactions (Prof. Dr. Henning Urlaub)
Biological function frequently depends on proteins interacting with other proteins, with RNA/DNA or with small organic ligands. XL-MS has recently been established as a major tool to elucidate not only interactions between, but the actual contact sites of proximal proteins within biomolecular complexes. Bifunctional cross-linking reagents are used to establish covalent links between reactive groups of proteins in close proximity. Following enzymatic digestion to peptide-peptide cross-links, these can be identified using high resolution LC/MS/MS analysis and dedicated database searching algorithms. The resulting information about spatially proximal amino acid residues can then be used to derive information about the composition, stoichiometry or – in combination with other methods such as NMR or cryoEM – even structure of biomolecular complexes.
Our group applies a range of cross-linking reagents, methods and computational approaches to the elucidation of protein-protein interactions in complex biological systems such as large functional complexes (e.g., the spliceosome), cellular compartments or even whole cells.
Data independent acquisition mass spectrometry (DIA-MS) in clinical proteomics (Dr. Christof Lenz)
DIA-MS in proteome analysis is a data acquisition paradigm where quantitative information on peptides and proteins is not dependent on successful sequencing events, but is permanently recorded for the whole protein and peptide complement of each biomedical sample. Information on sequence is infered from pre-recorded MS/MS spectral libraries to control false detection rates (FDRs). As DIA-MS can produce extremely consistent quantitative data on large numbers of biological samples, it is particularly suited for clinical proteomics using large sample cohorts.
We have successfully established DIA-MS as a tool for proteome studies not only in cell culture, but specifically also in mammalian tissues and body fluids. In conjunction with pressure cycling technology (PCT)-based tissue lysis, global proteome profiling by DIA-MS in e.g. brain or cardiac tissues enables detailed insights into the molecular basis of many disease processes both in model systems and in patient samples.
Complexome profiling and proximity labeling for the analysis of stable protein complexes (Dr. Christof Lenz)
Interactions between proteins that produce biological function may be interrogated on multiple levels. Beyond classical affinity purification mass spectrometry (AP-MS) experiments that provide information about direct protein-protein interactions, proximity labeling mass spectrometry (PL-MS) may be used to derive information about proteins in the wider spatial proximity of proteins of interest. Using specifically designed fusion constructs, reactive radical species are produced in the proximity that covalently modify proteins with biotin residues, which may in turn be used to purify these proteins and identify them by LC/MS/MS. Especially in restricted cellular compartments, PL-MS approaches provide highly detailed information on the functional environment of proteins.
On another level, stable biomolecular complexes may be separated under non-denaturing, “close-to-native” conditions using either Blue Native gel electrophoresis (BN-PAGE) or size exclusion chromatography (SEC). Following fractionation, intact complexes may be detected and quantified using label-free mass spectrometry and either unbiased hierarchical clustering or complex composition hypotheses drawn from publicly available protein interaction databases. We have successfully established the use of DIA-MS for highly reproducible protein quantitation across fractions, and have applied this workflow to e.g. high MW protein complexes from human and mouse membrane separations.
Methods are usually developed as research collaborations, and are then transferred to the Core Facility Proteomics to be made available to researchers across the UMG and the Göttingen Research Campus.