Data for: MS2 and LC libraries for untargeted metabolomics: Enhancing method development and identification confidence

Published: 17-04-2020| Version 1 | DOI: 10.17632/9m89d3wjj5.1
Markus Schwaninger,
Kimberly Begemann,
Julica Folberth,
Alaa Othman,
Olaf Jöhren


The MS² library includes over 4,000 fragmentation spectra of 506 standard metabolites for 6 different normalized collision energies (NCEs). A list of compounds is provided in the related supplementary material. The data was generated with an Orbitrap mass spectrometer (QExactive, ThermoFisher Scientific, Bremen, Germany). The data format (.db) is compatible with Library Manager (ThermoFisher) or mzVault (ThermoFisher). The MS² library will be available in an open access format on the Website of our group ( The LC library includes information about the chromatographic behavior of 294 metabolites. A total score and scores for sensitivity, peak width, peak asymmetry and retention are listed. For the score system, please see the related manuscript/supplementary material. Retention factors (k values) and retention times are available as a resource for elution order. The LC library ID corresponds to Table S2 of the related manuscript/supplementary material. It is possible to filter for one or more metabolites of interest in order to find the most suitable method for analysis.