BayBioMS - Semi-targeted Metabolomics

In semi-targeted metabolomics, the researcher is looking for related compounds of a known compound class. Preferably these compounds have a characteristic fragmentation pattern, so that neutral loss scans, precursor ion scans or data-dependent or -independent fragmentations help to identify the structural related compounds.

The neutral loss scan identifies molecules which have a common neutral fragment like the loss of sugar moieties. The precursor ion scan extracts molecules which generate a common charged fragment. In case of the data-dependent or –independent fragmentation the complete MS/MS spectra is compared to databases like GNPS (

Literature Example

Kleigrewe, K.; Almaliti, J.; Tian, I. Y.; Kinnel, R. B.; Korobeynikov, A.; Monroe, E. A.; Duggan, B. M.; Di Marzo, V.; Sherman, D. H.; Dorrestein, P. C.; Gerwick, L.; Gerwick, W. H., Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria. J. Nat. Prod. 201578, 1671-82.

Niehaus, E. M.; Kleigrewe, K.; Wiemann, P.; Studt, L.; Sieber, C. M.; Connolly, L. R.; Freitag, M.; Guldener, U.; Tudzynski, B.; Humpf, H. U., Genetic manipulation of the Fusarium fujikuroi fusarin gene cluster yields insight into the complex regulation and fusarin biosynthetic pathway. Chem. Biol. 201320, 1055-66.