IMSC service and user fee structure (updated March 7, 2024)

The general policy of the IMSC is to provide high-level mass spectrometry (MS) service to every scientist and research group from the RUG and UMCG to the best of our abilities. All MS instruments and associated equipment are operated, supported and supervised by one or more IMSC technicians, employed by RUG or UMCG. Exploitation of the IMSC, notably repair and maintenance of MS equipment, and costs of MS-specific consumables is covered by user fees. It is also used for small investments and instrument upgrades.
The personnel of IMSC together with the core partners Analytical Biochemistry (GRIP, RUG) and Pediatrics (UMCG) are continuously applying for new funds to refresh the instrument park and research infrastructure and strive to implement new analysis methods in the field of proteomics and metabolomics. The latest developments that we are working on are in the field of high throughput DIA analysis of clinical samples, glycomics and single cell proteomics.
Starting September 1, 2023 we work with a sample-based fee system,  The fee per sample depends on the type of analysis. We distinguish three main categories:

  • Proteomics                              100 euro per sample

This includes shotgun proteomics, quantitative workflows such as LFQ and TMT as well as SRM-based quantification of multi-protein panels using stable-isotope labelled standards.

  • Metabolomics                           50 euro per sample

This includes complex untargeted metabolite analysis of the metabolome, lipidome and exposome as well as label-free feature-based quantification.

  • Compound-specific analysis  10 euro per sample (minimum charge 50 euros)

This includes both LC-MS/MS SRM-based quantification using stable-isotope labelled standards as well as exact mass determination & confirmation by flow injection or fast LCMS. Both small molecules (metabolites, drugs, synthesized compounds) and intact proteins are covered. The minimum charge is 50 euro per submitted batch of samples to cover preparation time.


  • Special reagents including (isotopically labelled) standards will be included at cost if they are not provided by the customer directly. This will be discussed before analysis.
  • Consumables such as SPE columns and LC columns, for standardized protocols for proteomics and metabolomics are included in the per-sample rates. Special, expensive consumables will be included at cost if they are not provided by the customer directly.  This will be discussed before analysis.
  • For compound-specific SRM-based quantitation blanks, QCs and calibration samples that are integral to the analysis are counted as samples for the cost calculation.
  • If multiple LC-MS(/MS) methods are used for the same physical sample, e.g. positive mode and negative mode for metabolomics, each injection is regarded as a separate analysis i.e. sample.
  • Method development for SRM-based quantitation of novel metabolites or matrices is time-consuming and time investment is not easily predictable. The quality targets for the analysis will be discussed with the customer before and during development. Per method development day, a fee of 400 euro is charged.
  • Data analysis using standard data processing pipelines (e.g. PEAKS, Spectronaut, MaxQuant, SkyLine) is included in the per-sample rate.
  • For external customers (non-RUG or UMCG) overhead and personnel costs are added and the per-sample fee is multiplied by 4.


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