Our group applies mass spectrometry-based proteomics to quantitatively investigate and compare the cellular proteome under various conditions. We continuously advance our analytical workflows to address fundamental research questions at the interface of biochemistry and medicine. In addition to pursuing our own research topics, we actively contribute our expertise in mass spectrometry to collaborative scientific projects.

We are currently establishing a Proteomics Core Facility at the Medical Faculty of the University of Augsburg to provide state-of-the-art proteomic services and foster interdisciplinary research.

Quantitative Proteomics

For protein quantification, we employ a range of complementary strategies, including:

• Label-free quantification (LFQ) (Pradhan et al., 2022, Redox Biology)
• Stable isotope labeling with amino acids in cell culture (SILAC)(Konze et al., 2017, J. Proteome Res.)
• Tandem mass tag (TMT) labeling (ongoing projects)

These approaches enable robust, reproducible, and multiplexed analysis of proteomic changes across different biological conditions.

Subcellular Localisation

Beyond whole-cell proteomics, we implement specialized methods to enrich proteins from defined cellular compartments.

• To investigate the cell surface proteome (surfaceomics), we apply periodate oxidation followed by aniline-catalyzed oxime ligation (PAL), which allows biotin-tagging of glycoproteins and efficient enrichment of highly pure surface (glyco)proteins (Konze et al., 2017, ChemBioChem).
• To study secreted proteins (secretomics), we optimize cell culture conditions (e.g., serum-free media) and apply tailored precipitation protocols to isolate proteins from the extracellular milieu (Wolling et al., 2018, Proteomics)

Protein Modifications

A major research focus of our group is the analysis of protein glycosylation, including:

• C-mannosylation (Kespohl et al., 2024, FEBS J; Cirksena et al., 2021, Mol. Cell. Proteomics)
• O-glycosylation (Pandey et al., 2018, Glycobiology, Lee et al., 2013, PloS Genet; Sethi et al., 2012 J Biol Chem, Sethi et al 2010, J Biol Chem)
• Methylation (Marquardt et al., 2025, FEBS Lett)
• N-glycosylation (ongoing projects)

To achieve detailed characterization, we combine various fragmentation methods with dedicated bioinformatics tools and leverage our long-standing expertise in glycobiology.

Bioinformatics

We are experienced in bioinformatic analysis and biological interpretation of generated (multi)OMICs-data and increase general understanding at a level of systems biology.