Proteomics

Over the years shotgun proteomics has become a powerful tool allowing protein identification and quantification in a robust and high-throughput manner. The Proteomics Core Facility (PCF) provides profound expertise and infrastructure to support scientists with their projects. Our core competence comprises shotgun proteomics experiments aiming to sensitively detect and quantify changes in protein expression, protein modifications, and protein interactions. Equipped with state-of-the-art Quadrupole-Orbitrap mass spectrometers (MS), along with experience in most recent sample preparation protocols and bioinformatics approaches, our facility matches highest proteomics standards.

Shotgun proteomics-label-free quantification workflow: During sample preparation proteins are extracted from biological sources and digested into peptides. The complex peptide mixture is the separated on a HPLC system connected online with the mass spectrometer. Here gaseous peptide ions are separated according to their mass-to-charge ratio. In a typical liquid chromatography-mass spectrometry (LC-MS) experiment thousands of MS spectra are acquired. For quantification of peptide/protein intensities across samples, the elution profile of peptides are detected and compared to the same peptides in a different LC-MS run. Using statistical software label-free quantification data are further evaluated and visualized.

In addition to protein identification services, we have set up a sensitive label-free quantification workflow that allows relative protein quantification across different MS runs. Our facility is dedicated to continuously adapt, develop and implement strategies aiming to provide optimal analytical solutions.

Among the established proteomics approaches are:

Protein identification from purified proteins, protein in-gel and whole cell extracts
Relative proteome quantification and estimation of absolute protein abundances using label-free quantification
Precise absolute protein quantification using labeled peptide standards
Small scale and large scale interaction studies (e.g. protein-protein interaction and/or protein-ligand interactions)
Analysis of protein modification for enriched proteins and on a global scale (e.g. phosphoproteomics)

In order to provide the best analytical solution to the project needs, we favor an open communication structure, in which the PCF is preferably involved in early planning steps. Based on established procedures, we design project oriented adjustments to match individual project specifications. Furthermore, given the complexity of proteomics workflows, scientists are trained in sample preparation. Projects can be discussed with Dr. Timo Glatter.

PLEASE CONTACT THE CORE FACILITY STAFF BEFORE PERFORMING PROTEOMICS EXPERIMENTS!