Radboudumc Technology Center Mass spectrometry

Peptide mixtures are separated using C18 reversed phase nanoflow liquid chromatography using the EvoSep One liquid chromatograph. Peptides eluting from the column are measured using data-independent acquisition Parallel Accumulation Serial Fragmentation (dia-PASEF) by the timsTOF Pro2 mass spectrometer.

Data processing is performed in real-time using the Spectronaut search engine (ProteinScape) for fast turnaround time. The customer will receive an MS Excel file with protein identification and label-free quantitation result tables, raw datafiles, and materials & methods documentation.

Results will be sent to customers within 3 weeks after we have received the samples. Please contact us if you plan to use this service and to receive a quote.

To submit samples for proteomics you first need to contact us to register your samples. Please use the contact form at the top of our RTC page if you would like to discuss possibilities.

If needed, a short intake meeting will be scheduled to align services with the customer. Following registration and quotation, you may proceed with sample preparation and schedule an appointment for sample transfer. It is possible to submit either protein extracts or protein digests for proteomics. For available protein extraction protocols or in case of questions, you can contact us as well.

Guidelines for samples

• Samples should not contain any particles or cellular debris.
• Avoid the use of detergents and polymers (e.g. SDS, BRIJ 35, NP40, triton x-100, PEG) if possible. Please inform us when detergents or polymers are required for your sample preparation.
• The customer needs to perform protein quantitation (e.g. using nanodrop or micro bca kit) themselves.
• Recommended protein amount and concentration: at least 10µg protein at a concentration of 0.1-10 µg/µl.

NWO National Roadmap Large-Scale Research Infrastructure roadmap project combining technologies in the field of genomics, proteomics, metabolomics and data analysis, integration & stewardship (2018-2029).

More information can be found on this website.

Public-private partnership project to develop glycan database free glycoproteomics software solutions (2025-2028).

Health-Holland public-private partnership project to develop real-time data processing solutions for implementation of (glyco)proteomics technology in clinical environments (2021-2025).

Stofwisselkracht project to establish multi omics readout platform for patient derived 3D engineered heart tissues (2023-2025).

United for Metabolic Disease project to establish a multi omics platform for inborn errors of metabolism biomarker discovery (2020-2024).

ZonMw medium investment project to establish (pre-)clinical glycoproteomics platform (2019-2023).