Metabolomics

Methods

The analysis of primary metabolites (e.g. organic acids, amino acids, nucleotides, energy and redox cofactors) and xenobiotics is done by untargeted metabolomics, which allows to detect thousands of features in parallel, including unexpected compounds. We offer two standard configurations:

1) Untargeted metabolomics by LC-MSn

This approach includes a chromatographic separation that allows to discriminate between compounds with similar mass and reduce the interferences in complex samples. Specificially, we use a custom quaternary gradient that wss optimized to separate metabolites of all classes and chemical properties (up to logP <8). A sequence includes acquisition of MS2 data for structural confirmation, library matching, etc. This is the recommended approach for clinical or complex samples, and for all studies with < 5000 samples.

2) Untargeted metabolomics by flow injection (FIA)-MS

In flow injection analyses, the chromatographic separation is omitted. Thereby, much higher throughputs can be achieved at the cost of distinguishing compounds with the same molecular formula. This method is a unique speciality of our lab. The method was originally developed in 2011 and continuously improved with hardware and software ameliorations to maximize sensitivity and robustness. Over more than a decade we analyze ca. 1.5 Mio samples and published external page> 100 paperscall_made. The largest study performed was with ca. 75'000 samples. This is the recommended approach for the analysis of cellular extracts (i.e. primary metabolism) or supernatants. 

Notes:

• The FIA method is about 75% cheaper than the LC-MSn method.
• All readouts are semi-quantitative, i.e. provide relative changes of each detectable compound across the study. On demand and for limited compounds, approximative amounts (concentrations) can be approximated by spiking isotopically labeled (²H or ¹³C) standards.
• Both methods can be run in either negative or positive mode. Normally, we recommend to use negative mode only in the analysis of most sample types. Analysis in positive mode is only recommended for the analysis of low abundance polyamines.