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.

Sotgun-Proteomik-markierungsfreier Quantifizierungsworkflow: Bei der Probenvorbereitung werden Proteine aus biologischen Quellen extrahiert und zu Peptiden verdaut. Die komplexe Peptidmischung wird auf einem HPLC-System getrennt, das online mit dem Massenspektrometer verbunden ist. Dabei werden gasförmige Peptidionen nach ihrem Masse-Ladungs-Verhältnis getrennt. In einem typischen Flüssigchromatographie-Massenspektrometrie (LC-MS)-Experiment werden Tausende von MS-Spektren erfasst. Zur Quantifizierung der Peptid-/Proteinintensitäten über die Proben hinweg wird das Elutionsprofil von Peptiden erfasst und mit den gleichen Peptiden in einem anderen LC-MS-Lauf verglichen. Mit Hilfe statistischer Software werden markierungsfreie Quantifizierungsdaten weiter ausgewertet und visualisiert.

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.


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