liulime / report

This repository contains training data for retention time prediction for the identification of metabolites from non-targeted LC-MS based metabolomics

RepoRT

Important

Git LFS has now been disabled for the majority of the contents of RepoRT for better traceability of changes. It might be necessary to "force-pull" the repository, if you already have a local version. Alternatively, simply clone/download the repository again, if experiencing difficulties. A mapping from old to new commit hashes is available here.

RepoRT is a repository dedicated to the collection of training data for the development of new retention time prediction models for the identification of small molecules. It is part of the collaborative project between Prof. Dr. Sebastian Böcker (Friedrich-Schiller-Universität Jena) and Dr. Michael Witting (Helmholtz Zentrum München) fundend by the DFG (Project Number 425789784, DFG GEPRIS).

We are collecting information such as retention time (RT) and chemical structures of small molecules in standardized format. From the input data structures are standardized using the PubChem standardization and molecular fingerprints and chemical descriptors are calculated using rcdk. Classification of molecules is performed using ClassyFire. Additionally, to chemical information on the measured small molecules, metadata on the chromatographic separation is collected, e.g. column, column dimensions, flow rate, gradient, eluents and their exact composition. The exact format is explained here.

We are covering all possible separation modes of liquid chromatograpy (LC), such as Reversed-phase (RP), Hydrophilic iinteraction Liquid Chromatography (HILIC) and others. The plot below show the current coverage of different separation modes and columns.

ToDo: add plot here

Contributing data

We are welcoming data submissions. If you want to submit data to this repository, please get in contact with Michael Witting ([email protected]{.email}).

Contributors

The following people and resources contributed training data for this repository.

Collections:

• PredRet
• Phenome Centre

Publications:

• J. Folberth et al.
• J. Pezzatti et al.
• X. Domingo-Almenara et al.
• R. Stoffel et al.

People:

• Serge Rudaz, University of Geneva
• Eva-Maria Harrieder, Helmholtz Munich
• Carolin Huber, UFZ
• Maria Eugenia Monge, CIBION-CONICET
• Jörg Büscher, Max Plank Institute of Immunobiology and Epigenetics
• Aneli Kruve, Stockholm University