Our Research Support and Equipment
We offer 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 (e.g. Sequest, Pulsar) and software packages (Proteome Discoverer, Byonics, Spectronaut and MaxQuant).
Protein identification
Identification of proteins from a complex mixture (e.g. cell lysate), or verification of a (modified) amino acid sequence from a highly purified protein can be performed by the Proteomics Core Facility.
Relative protein quantification
Global quantitative proteomics is a powerful strategy for unbiased analyses and understanding protein-level changes as well as modification profiles (e.g. phosphorylation) in biopsies, cells, body fluids, or other biological materials. This approach provides critical insights into global protein expression patterns, revealing the molecular mechanisms underlying biological processes and their dynamics.
Absolute protein quantification
The ProteomEdge™ technology allows absolute quantification of up to hundreds of selected proteins from biological and clinical samples.
During sample preparation, recombinant human protein fragments containing heavy isotopes of lysine and arginine (13C and 15N) are introduced. These labeled fragments act as internal protein standards (qRePS™), which are quantified in parallel to their non-labeled endogenous counterparts using Parallel Reaction Monitoring (PRM) LC–MS, a highly sensitive and selective mass spectrometry method.
Clinical Proteomics Platform for Precision Medicine
The advancement of sensitive and high-throughput Data-Independent Acquisition mass spectrometry (DIA-MS) technologies has enabled the analysis of large cohorts —an essential capability for precision medicine and translational research. PCF is one of the sites for the national Clinical Proteomics Technology Platform at the BioMS and SciLifeLab infrastructures.
Applications
- Research: Deeper understanding of biological processes and disease mechanisms by profiling the proteome.
- Diagnostics and Molecular Phenotyping: Identification of biomarkers and disease-specific protein signatures for various conditions
- Precision Medicine: Proteomic profiling supports clinical decision-making and tailoring of treatments based on each individual’s unique molecular profile, e.g. digital or molecular twin.
- Drug Development: Discovery of novel therapeutic targets, assessment of drug efficacy, and monitoring of treatment responses.
Fresh frozen tissue or FFPE proteomics
Large-scale, reproducible, and quantitative proteomic profiling from fresh frozen tissue and formalin-fixed paraffin-embedded (FFPE) specimens.
Plasma proteomics
High-throughput, reproducible and clinically relevant data for biomarker discovery, disease understanding, and precision medicine from plasma.
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 other post-translational modifications are ubiquitination, methylation and acetylation. Thus, even probe-specific binding to a target protein can be examined and validated using LCMS.
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
- Thermo KingFisher Apex
- Cellenion CellenONE
Chromatographic systems
- online: Thermo Easy nLC1200 systems
- online: Evosep One/Eno nLC systems
- online: Thermo Vanquish Neo systems
- offline: high pH UPLC fractionation: Thermo Dionex Ultimate 3000
Mass spectrometers
- Bruker timsTOF SCP
- Bruker timsTOF HT
- Thermo Orbitrap Astral
- Thermo Orbitrap Eclipse Tribrid
- Thermo Orbitrap Fusion Lumos Tribrid
- Thermo Orbitrap Fusion Tribrid
- Thermo QExactiveHF
- Thermo Orbitrap LTQ