Our Research Support and Equipment
We offer research support including study design, protein identification, characterization of post-translational modifications, and protein interaction analysis. Global quantitative analyses of differentially expressed proteins reflect the majority of our projects.
The Proteomics Core Facility has experience regarding preparation of a huge range of samples originating from tissues, cells, isolated cellular compartments, pull-downs, other biological samples, or expressed proteins. The facility is equipped with the latest high-resolution mass spectrometers.
We provide comprehensive data analysis through a variety of database search engines (Mascot, Sequest, Pulsar) and software packages (Proteome Discoverer, Byonics, Spectronaut and MaxQuant).
Protein identification
Identification and determination of sequence coverage of a highly purified protein or identification of proteins in a complex mixture is a service provided by the Core Facility.
Quantitative Mass Spectrometry
Quantitative proteomics includes powerful global discovery or targeted methods to analyze and understand protein changes in cell, tissue or other biological material.
Post-translational modifications
Protein post-translational modifications (PTMs) are chemical modifications that regulate cellular activity and influence the molecular mechanisms of biological processes and disease states. The main challenge studying PTMs is that they are low abundant. PTMs of purified proteins or a highly expressed proteins can be characterised by mass spectrometry directly, while PTMs in complex samples have to be enriched for prior to the MS-analysis.
Glycosylation
Protein glycosylation is one of the most common and the most complex post-translational modification.
Phosphorylation
Phosphorylation is one of the most common post-translational modification. Cells tightly control phosphorylation of proteins by an interplay beweeen kinases and phosphatases, creating a fast, powerful, and transient mechanism adapting cellular processes in response to stimuli.
Other modifications
Any modification of proteins can be studied as long as the exact composition of the modification is known. The mass shift of the modification is entered manually into the database and used in the database matching. Common post-translational modifications are ubiquitination, methylation and acetylation.
Interaction or network analyses
Proteins rarely act alone, and their functions are regulated by interacting partners. Protein-protein interaction (PPIs) databases provide known and predicted protein-protein interaction networks.
Immunoprecipitations are performed using antibodies for protein-of-interest isolation; whereas affinity purifications and pull-down experiments are done using a tagged bait like RNA or peptides.
Equipment
Automated sample preparation
- Beckman Coulter Biomek i7
- Cellenion cellenONE
Chromatographic systems
- online: Thermo Easy nLC1200 systems
- online: Evosep One nLC systems
- online: Thermo Scientific Vanquish
- offline: high pH UPLC fractionation: Thermo Dionex Ultimate 3000
Mass spectrometers
- Bruker timsTOF SCP
- Bruker timsTOF HT
- Thermo Orbitrap Eclipse Tribrid
- Thermo Orbitrap Fusion Lumos Tribrid
- Thermo Orbitrap Fusion Tribrid
- Thermo Orbitrap Exploris 480
- Thermo QExactiveHF
- Thermo Orbitrap LTQ