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

Julica Folberth, Kimberly Begemann, Olaf Jöhren, Markus Schwaninger*, Alaa Othman

*Corresponding author for this work
1 Citation (Scopus)


As part of the “omics” technologies in the life sciences, metabolomics is becoming increasingly important. In untargeted metabolomics, unambiguous metabolite identification and the inevitable coverage bias that comes with the selection of analytical conditions present major challenges. Reliable compound annotation is essential for translating metabolomics data into meaningful biological information. Here, we developed a fast and transferable method for generating in-house MS2 libraries to improve metabolite identification. Using the new method we established an in-house MS2 library that includes over 4,000 fragmentation spectra of 506 standard compounds for 6 different normalized collision energies (NCEs). Additionally, we generated a comprehensive liquid chromatography (LC) library by testing 57 different LC-MS conditions for 294 compounds. We used the library information to develop an untargeted metabolomics screen with maximum coverage of the metabolome that was successfully tested in a study of 360 human serum samples. The current work demonstrates a workflow for LC–MS/MS-based metabolomics, with enhanced metabolite identification confidence and the possibility to select suitable analysis conditions according to the specific research interest.

Original languageEnglish
Article number122105
JournalJournal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences
Pages (from-to)122105
Publication statusPublished - 15.05.2020

Research Areas and Centers

  • Academic Focus: Center for Brain, Behavior and Metabolism (CBBM)


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