UHPLC retention time and MS/MS mass spectral fragmentation libraries

The availability of high quality UHPLC retention time data as well as metabolite mass spectral fragmentation data in the metabolomics community is essential to provide high confidence metabolite annotations and identifications.

Two mass spectral fragmentation libraries are available below in .db (mzVault) format to be applied with Thermo Scientific’s Compound Discoverer software. Data were collected for mixtures of up to twenty chemical standards dissolved in solution applying predominantly HCD MS2 fragmentation. Data for greater than 500 metabolites is available in each library.

Retention time data is also available for each metabolite detected in two complementary UHPLC assays (HILIC and aqueous C18 reversed phase).


Positive ion mode mass spectral fragmentation libraryPositive ion mode_Jan2021.db
Negative ion mode mass spectral fragmentation libraryNegative ion mode_Jan2021.db
UHPLC retention time data for positive and negative ion modesACMG+TFS_MetaSci_UHPLCMS_RT library.xlsx
UHPLC, MS and raw data processing methodsData acquisition and processing methods


These data were collected and processed by Dr William Nash with significant assistance from Dr Elliott Palmer.

We would like to acknowledge and thank Thermo Fisher Scientific for technical support, provision of chemical standards and laboratory access at their San Jose site. Specific thanks go to Ioanna Ntai, Amanda Souza, Andreas Huhmer and Madalina Oppermann.

Other mass spectral fragmentation libraries are available and some include UHPLC retention time data also. We apply the following in our research: