A full-fledged proteomics facility, right at your finger tips.
Why proteomics?
Proteins are the prime executioners of all processes inside cells, ranging from gene expression regulation to cell division and cellular metabolism.
Importantly, deregulated protein functioning is a main driver of human disease. Therefore, identifying the cellular proteome or interaction partners for proteins of interest Is key to solving important biological questions in health and disease. Proteomics4Oncode offers mass spectrometry-based (interaction) proteomics expertise and service to help you answer your research questions.
The Proteomics4Oncode facility operates five state-of-the-art, high-resolution instruments: an Orbitrap Tribrid Eclipse, (soon) 2 Orbitrap Astral instruments and a Orbitrap Exploris 480 machine. These mass spectrometers can be used for a broad variety of applications, ranging from quantitative whole proteome measurements to post-translational modification (PTM) analyses (phospho, acetyl, etc.) and affinity purification of protein complexes. Next to these standard workflows we are also open to work with our customers on customized approaches to address specific questions such as protein or PTM turnover experiments or absolute whole proteome measurements. Furthermore, Proteomics4Oncode provides advice to help you design the best possible experimental setup for your research question. Finally, automated phospho-enrichment and offline chromatography workflows are also available upon request.
Costs
We are a non-commercial facility for the greater Oncode/life science community. To cover depreciation of the instrumentation, maintenance service contracts and local technical support, the facility charges a non-commercial price of €50 per hour of measurement time, plus half an hour of loading time per sample. When a certain experiment necessitates the use of expensive reagents, (such as TMT labels or UPS2 spike-in for absolute protein quantification) these will also be charged.
Furthermore, since experiments are done in collaboration with Proteomics4Oncode, these will result in joint publications between the facility and the ‘customer’.
Approaches
Experimental workflows
We provide the following experimental workflows:
(Phospho)proteomics (with relative or absolute quantification)
Protein affinity purification using epitope tags such as GFP, HA, FLAG or Myc tag
Peptide or DNA affinity purification (identification of proteins interacting with a specific (modified) peptide or DNA sequence of interest)
PAQMAN for the determination of apparent Kd of transcription factors for a specific sequence
Quantification
The following quantification strategies are available:
Label Free Quantification — Comparison of 2 or more conditions in triplicates, possibility to calculate stoichiometry for stable complexes.
Stable Isotope Labeling by Amino acids in Cell culture — SILAC, only for easy-to-culture cell lines.
Dimethyl labeling — For comparison of 2 or 3 conditions.
Isobaric TMT labeling — For comparison of >5 conditions.
Waste no time
Whether you’ve already worked out exactly what you need, or you’re still exploring your possibilities, we’re here to help. Reach out to proteomics@umcutrecht.nl if you have any questions, or fill out our inquiry form if you want to waste no time.
