FragHub: A mass spectral libraries data integration workflow

26 April 2024, Version 3
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Open mass spectral libraries (OMSL) are critical for metabolite annotation and machine learning, especially given the rising volume of untargeted metabolomic studies and the development of annotation pipelines. Despite their importance, the practical application of OMSLs is hampered by the lack of standardized file formats, metadata fields, and supporting ontology. Current libraries, often restricted to specific topics or matrices such as natural products, lipids, or the human metabolome, may limit the discovery potential of untargeted studies. FragHub addresses these challenges by integrating multiple OMSLs into a single comprehensive database, supporting various data formats and harmonizing metadata. It also proposes some generic filters for mass spectrum using a graphical user interface. Additionally, a workflow to generate in-house libraries compatible with FragHub is proposed. FragHub dynamically segregates libraries based on ionization modes and chromatography techniques, thereby enhancing data utility in metabolomic research. The FragHub Python code is publicly available under a MIT license, at the following repository: https://github.com/eMetaboHUB/FragHub. Generated data can be accessed at https://doi.org/10.5281/zenodo.11057687.

Keywords

Open mass spectral library
metabolomics
dereplication
Mass spectrometry
database

Supplementary materials

Title
Description
Actions
Title
supplementary table
Description
All supplementary table cited in the main text
Actions
Title
FragHub tutorial
Description
A tutorial to install and use the fraghub python workflow
Actions
Title
in-house database
Description
A tutorial to create an in-house database using MZMine
Actions

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.