About us

Research Unit Protein Science (PROT) – Core Facility Proteomics

Imbedded into the research mission of Helmholtz Centre Munich, the Research Unit Protein Science and its technical platform Core Facility Proteomics provide mass spectrometry based proteome analysis at an advanced scientific and technical level.

Our analytics oriented high-throughput competence platform can be applied to investigate biological systems and their specific disease associated alterations on the level of protein signatures (biomarkers) or functional protein interaction network. The Research Unit Protein Science and the facility are integrated into Helmholtz strategic programs and benefit from constant technology and methodology advancement and development within national research collaborations as well as industrial collaborations. The facility is furthermore well harmonized with HUPO standards and closely connected to the “Deutsche Gesellschaft für Proteomforschung”.

The Core Facility provides relevant details regarding proteomic approaches, instrumentation, and sample preparation (SOPs) online. With the implementation of a LIMS (Proteus) users have access to a web based platform for sample submission, monitoring of sample processing, project status, and result downloads.

The analytics portfolio covers sensitive qualitative approaches with LC-MS/MS (LTQ Orbitrap XL, QExactive-HF) instrumentation as well as versatile quantitative proteomic approaches. This includes metabolic labeling such as SILAC, as well as peptide-based labeling such as TMT and protein-based labeling such as ICPL. Furthermore, we offer peptide-intensity based label-free quantification of shotgun data as well as peptide or fragment-ion based label-free quantification of all ion fragmentation approaches. On request, targeted quantification approaches with or without the use of heavy isotope labeled peptides are available. For data analysis, a variety of bioinformatics solutions are available (Progenesis-QI, MaxQuant, ProteomeDiscoverer, OpenMS, Scaffold, Spectronaut, Skyline and more).