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Metabolomics Core Facility

This facility provides services for analysis of metabolites and lipids.

Guide to sample cleanup and storage

General minimum amount of material required

  • Cell culture: 1-2 million cells
  • Microbial pellet: 5-25 mg
  • Tissue: 5-25 mg (maximum: 50 mg)
  • Biofluids (plasma/ serum and urine): 20 μL

Note: For solid materials, the respective weights per sample must be provided in an electronic sample list

Recommended extraction solvents

  • Metabolites: methanol, acetonitrile, water
  • Lipids: methanol, isopropanol, MTBE

Please refer to our protocols for sample preparation for details.

Caution:

  • Use only LC/MS-grade solvents/water, additives, and buffers
  • Randomize the extraction order and balance all experimental groups across extraction days, batches and plates. E.g. do not process all controls first and all treated samples afterwards.
  • Provide a processed blank sample for blank filtering (sample without biological matrix of interest)
  • Please contact MCF staff for consultation regarding plastic laboratory tubes and sizes for your respective project
  • Use clean containers, sample tubes, laboratory tubes for sample processing and storage
  • Avoid glassware that has been cleaned with detergent e.g. from a laboratory kitchen. Cleaning of fresh glassware by rising multiple time with LC-MS grade solvents is required

Samples can be submitted as:

  • Dried extracts obtained using speedvac / blow-down nitrogen evaporators (drying preferred at cooled conditions or room temperature). Make sure to dry samples / supernatants after centrifugation only (at min. 10,000 g)
  • Monophasic extracts or initial extractions for subsequent biphasic extraction
  • Samples are to be shipped in sufficient dry ice.

Quality control

  • Include pooled quality control (QC) samples (without blank samples) with each batch of samples
  • Internal standards spiking during sample preparation: Deuterated or 13C/15N-labelled internal standards are an ideal choice – can be provided by MCF staff
  • Prepare biological replicates (minimum of 4 per condition are required)

Note: Please consult with MCF staff for the appropriate selection of the replicates, quality control samples, and internal standards that are suitable for your desired LC-MS analysis.

Storage & Shipment

  • Dried metabolite extracts should be stored at -80°C (optional filling with argon/nitrogen can help to prevent oxidation)
  • During processing, samples should be kept cooled (e.g. on ice)
  • Pack samples in dry ice for shipment
  • Use sample boxes and do not submit samples in plastic bags or just sitting on dry ice
  • In addition to any print outs, electronic sample lists must be provided
    • add all relevant metadata to the sample sheet (volume/weight of sample; experimental group/timepoint/etc. per sample)
    • add any extraction protocol performed at your site to the electronic file
    • final reconstitution solvent and volume
    • add information about the requested service to the sample list
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