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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
  • Biofluids (plasma/ serum and urine): 50 μL

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, additives, buffers and MilliQ nanopure water
  • Avoid contact with any plastic material during lipid extractions. Use glassware and glass syringes during lipid extraction.
  • The following plasticware can be used if required:
    • Eppendorf Safe-Lock Tubes, 2.0 mL (Part number 0030120094)
    • Eppendorf Safe-Lock Tubes, 1.5 mL (Part number 0030120086)
    • Eppendorf® twin-tec PCR plates 96 eppendorf (Part number Z651486)
  • Use clean containers, sample tubes, Eppendorf tubes for sample processing and storage
  • Avoid glassware that has been cleaned with detergent e.g. from the EMBL kitchen, or clean them several times with MilliQ water and MS-grade organic solvents prior to usage.

Samples can be submitted as:

  • Dried extracts obtained using speedvac / under nitrogen (preferred at cool conditions or room temperature)
  • Aqueous methanolic extracts
  • For outstations: please ship samples in sufficient dry ice.

Recommended reconstitution solvents

  • Water (50─80%)
  • Aqueous methanol/acetonitrile (20─80%)
  • Isopropanol
  • Methanol (caution: volume changes due to solvent evaporation at room temperature)
  • Minimum reconstitution volume 50-100 μl

Quality control

  • Do include pooled QC samples with each batch of samples for bracketing during analysis.
  • Internal standards spiking during sample preparation: Deuterated or 13C internal standards are an ideal choice.
  • Prepare replicates, preferentially biological and preparation replicates

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.

Before sample submission, make sure that:

  • extracts are completely soluble reconstitution solvents
  • samples are centrifuged above 10,000 g
  • there is no insoluble matter in samples
  • extracts are filtered if necessary (make sure to wash filters prior to usage, as some filter membranes contain stabilizing reagents)

Storage

  • Dried metabolite extracts should be stored at -80°C (optional filling with argon/nitrogen would help to prevent oxidation)
  • During processing, samples should be kept on ice
  • Pack samples in dry ice for shipment times of more than 1 hour
  • Samples will be kept at 4°C during LC-MS analysis
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