Sample preparation

Sample preparation usually involves the following steps, also depicted in Figure below:

  • collection
  • storage
  • extraction
  • preparation
  • custom preparation for individual measurement systems, e.g. derivatisation for gas chromatography
Figure 6 Main steps involved in sample preparation

Extraction techniques

Solid-phase extraction (SPE)

SPE is a process whereby compounds which are dissolved or suspended in a liquid mixture are separated from other compounds according to their chemical and physical properties. SPE is often used in metabolomics laboratories to concentrate and purify a sample.


Chromatography is an important step in metabolomics experiments to separate individual metabolites from a mixture. The most common technologies used in mass spectrometry are gas and liquid chromatography. Through interactions of analytes with a mobile and stationary phase, compounds are separated and elute off the chromatographic column at different time points, based on their physio-chemical properties.