Sample Preparation

To ensure that metabolomics data support the project aims, an appropriate sampling of relevant biological or clinical specimens, beside the proper choice of the analytical method, is essential. It is clear that these steps of the metabolomics workflow are in the full responsibility of the applying project teams or users. However, the FGCZ has considerable expertise on these issues and recommends to involve the responsible FGCZ staff already in the planning of projects which include metabolomics or metabonomics.

What might be considered at this stage?

Is the final interpretation on the subcelluar, cellular or organism level? The answer should giude the choice of a representative specimen, i.e. subcellular fraction(s), cells (cultures, tissues) or body fluids.
Should the final interpretation be based on qualitative, relative or absolute quantitative data? The answer may give clues about the necessity and design of in situ labelling and replication.
Are you looking for new biomarkers and indicative patterns or do you start with a well defined metabolic model? The answer may let you choose between an untargeted semi-quantitative or a targeted quantitative analysis.

What is to notice?

In tissues or cell systems (cell cultures) different phenotypes or morphotypes may be present. These can be sorted out and analysed seperately. The FGCZ has the facilities to support this task. In a recent project, mouse kidney tubular cells with a specific modification were isolated out of mixture of normal and modified cells.

Terminating biochemical activity in collected specimens and their conservation is crucial for the analytical outcome. The FGCZ may advise users in finding effective solutions which do not interfere with the analysis of the metabolites.

Metabolites of cell or tissue samples have to be extracted. Body fluid samples require a pretreatment in order to eliminate irrelevant and undesired components present in excess, i.e. salts (e.g. urine), proteins (blood, cerebrospinal fluid). Additionally the isolation and concentration of a specific chemical class might be indicated, i.e. organic acids, lipids or others. The FGCZ provide protocols for, desalting, proteine precipitation as well as for the isolation of small polar metabolites and of divers lipid classes from a variety of biological specimens.

Support Mode

Projects are supported in User lab mode.

Contact

Endre Laczko