Activities and services
The Facility provides assessment of protein composition of a
variety of samples. Preferably, researchers first discuss with us
the project(s) they have coming up, in order to design the optimal
experimental setup allowing successful analysis by liquid
chromatography-coupled tandem mass spectrometry (LC-MS/MS). For
quantitative proteomics experiments, stable isotope labeling at the
peptide or protein level can be considered.
After performing the experiment, researchers hand in their
samples, which we process further for LC-MS/MS. Sample processing
involves protein extraction, reduction, alkylation, proteolytic
digestion, (optional) multiplex stable isotope labeling and
desalting. Finally, peptides are separated by nanoflow
reversed-phase liquid chromatography, and analyzed by tandem mass
spectrometry. After mass spectrometry analysis, MS/MS spectra are
processed with dedicated software to yield protein identification
(and quantification, if applicable). Results are exported as Excel
workbook and shared with the researcher. Limited bioinformatics
analysis can be discussed for further data interpretation.
What we take:
- cell pellets or cell lysates;
- protein fractions;
- immunoaffinity beads or eluates from
- SDS-PAGE gels*.
- Other sample types? Come and discuss the
*We prefer to run SDS-PAGE gels ourselves and cut gel bands here
at the Facility, so if you're interested in analyzing specific
bands, we'd like you to provide protein samples rather than a
What we offer:
- Quantitative & Qualitative (full) proteome
- Phosphoproteome analysis;
- Ubiquitinated proteome analysis
- Other requests? Come and discuss the
- Targeted protein quantitation (parallel reaction
Internal projects are on a collaborative basis and free of
charge, fitting within the capacity and scope of the facility.
However, certain expensive reagents (kits, antibodies etc.) may
have to be purchased by the researcher.
Unfortunately, most detergents are not compatible with
downstream mass spectrometry analysis. Dilution, washing, and
detergent removal columns cannot remove enough of these
contaminants for successful analysis of your sample or to prevent
massive contamination of the mass spectrometer and LC system.
Please talk to us about any detergents that are used in your sample
preparation procedure, even if they are far upstream in your sample
Thermo Orbitrap Fusion, a Q-OT-qIT hybrid mass spectrometer,
equipped with a Proxeon nLC-1000 nano-LC system.