Interfaculty Mass Spectrometry Center (IMSC)

Samples for MS analysis can be submitted by sending them to the IMSC facility in the ERIBA building (lab 3226.0650) or by sending an email to the IMSC email address. A sample form can be downloaded here.

Please contact us before sending samples to discuss the desired sample preparation and analysis details.

The type of service, contribution and collaboration depend on the type of research project and the input from the research group:

1. Scientists that wish to have samples analyzed on a regular basis, with questions that do not require extensive methods development, will usually interact directly with the technical staff of the IMSC and have their analyses done for the standard per-sample fee as outlined above.
2. Scientists that have research questions which require extensive methods development discuss first with the head of the IMSC (Hjalmar Permentier), and, if necessary, the scientific head (Peter Horvatovich), to define the approach and workload. Users will have to contribute financially to the method development work at least on a partial basis, by paying the regular fees. In the case of long-term developments (e.g. 3 months or more), which will also enhance the overall competence of the IMSC, an agreement can be made for a fixed fee according to agreed-upon criteria but will be lower than the cumulative per-sample fees. It is strongly recommended that users foreseeing such a use of the IMSC discuss their project needs prior to applying for funding and include the cost in their regular project budget.
3. Scientists that have research questions where the use of cutting-edge biological mass spectrometry and related techniques is required on a structural basis collaborate with the IMSC and the Analytical Biochemistry group on a scientific level. This implies, in general, that the IMSC and/or AB is already involved at the stage of the grant application and that costs for the use of instrumentation and consumables are part of the project budget. Joint grant applications and jointly supervised PhDs or postdocs are also welcomed and are drivers of implementation of novel mass spectrometry approaches. Specific bioinformatics analysis and workflows are being developed in-house such as for MS1/MS2 proteomics, metabolomics and stable isotope labelled data quantification with PASTAQ, proteogenomics data integration.
4. Scientists and commercial parties from outside the University of Groningen or the UMCG will be classified in the same way as internal academic users, but the user fees include salary cost and instrument depreciation, or agreed-upon contract criteria as mentioned above.
5. In all cases, IMSC expects to be acknowledged in publications, using our full details (Interfaculty Mass Spectrometry Center, Groningen, The Netherlands), and optionally the names of contributing IMSC personnel. Co-authorship is appreciated if we have made a significant scientific contribution to a publication.

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.

Notes:

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.