University of Gothenburg
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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) and software packages (Proteome Discoverer, Byonics 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.

TMT-18plex and label-free quantification is displayed
Isobaric labeling or label-free quantification (refer to www.thermofisher.com, www.bruker.com).

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.

displaying all different kinds of PTMs
Post-translational modifications of proteins. Source: https://www.creative-proteomics.com/blog/index.php/strategies-for-post-translational-modifications-ptms/

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. 

proteins are purified from complex mixtures using specific antibodies
The principle of Immunoprecipitation. Source: https://www.antibodypedia.com/text/text_methods.php?text=method_ip

Equipment

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

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