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Proteomics facility

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 immunoprecipitations;
  • SDS-PAGE gels*.
  • Other sample types? Come and discuss the possibilities!

*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 gel.

What we offer:

  • Quantitative & Qualitative (full) proteome analysis;
  • Phosphoproteome analysis;
  • Ubiquitinated proteome analysis
  • Other requests? Come and discuss the possibilities!
  • Targeted protein quantitation (parallel reaction monitoring).

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. 

Detergents

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 preparation protocol. 

Equipment 

Thermo Orbitrap Fusion, a Q-OT-qIT hybrid mass spectrometer, equipped with a Proxeon nLC-1000 nano-LC system.

 

 

Employees

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Liesbeth Hoekman

Technician

Experience

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Onno Bleijerveld

Postdoctoral fellow

Experience

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Altelaar, Maarten

Maarten Altelaar

Experience

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