Metabolome identification using LC-MSn Orbitrap-based mass spectrometry

Introduction Annotation of hundreds of unknown metabolites from human plasma is one of the most difficult challenges faced by metabolomics scientists.1 The degree of difficulty in the identification of unknown metabolites, however, depends on the information that can be extracted from an LC-MS dataset. An “unknown” feature is a single m/z and retention time observed during LC-MS analysis. This feature may be related to the chemical background from a blank sample and unrelated to the sample itself. Alternatively, a feature may be a real biological compound and its abundance changes in a control group compared to a treatment group. However, if this compound is not found in any compound database, it is referred to as an “unknown unknown”. When annotating unknowns using high-resolution accurate mass data, one can classify four distinctly different types of unknowns (Table 1): Authors: David Peake, Ioanna Ntai, Amanda Souza and Ralf Tautenhahn, Thermo Fisher Scientific, San Jose, California, USA