Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Chalcone-Terpene Hybrids from <i>Fissistigma litseifolium</i> (King) Merr as Potential Carbapenemase Inhibitors.

Journal of natural products·2026
Same author

2'-O-methylation-dependent installation of N<sup>2</sup>-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly.

Nature communications·2026
Same author

A Novel Peptides Database Approach for Enhanced Dereplication of Peptaibols Using Molecular Network Based on the <i>t</i>-SNE Algorithm.

Journal of proteome research·2025
Same author

Biomimetic Total Synthesis of Sarglamides A, B, C, Unnatural-Natural Sarglamide G, and Their Enantiomers.

Organic letters·2025
Same author

Phase separation in lead-saponified drying oils: Implications for historical painting techniques and paint stability.

Science advances·2025
Same author

Multimodal Analysis of Oak Wood Metabolites for a Comprehensive Understanding of the Aging Process in Typical French Spirit Barrels.

Journal of mass spectrometry : JMS·2025

Related Experiment Video

Updated: Feb 27, 2026

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
11:13

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

11.7K

MZmine 2 Data-Preprocessing To Enhance Molecular Networking Reliability.

Florent Olivon1, Gwendal Grelier1, Fanny Roussi1

  • 1Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Université Paris-Saclay , 91198, Gif-sur-Yvette, France.

Analytical Chemistry
|June 24, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces a new data preprocessing workflow to improve molecular networking analysis in metabolomics. The method enhances the Global Natural Product Social Molecular Networking (GNPS) platform by addressing limitations in isomer differentiation and chemical formula annotation.

More Related Videos

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

4.9K
Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures
09:38

Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures

Published on: January 7, 2019

9.2K

Related Experiment Videos

Last Updated: Feb 27, 2026

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
11:13

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

11.7K
Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

4.9K
Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures
09:38

Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures

Published on: January 7, 2019

9.2K

Area of Science:

  • Metabolomics
  • Computational Chemistry
  • Natural Product Discovery

Background:

  • Molecular networking is a popular technique for organizing tandem mass spectrometry (MS2) data in metabolomics.
  • Current tools like MS-Cluster on the Global Natural Product Social Molecular Networking (GNPS) platform have limitations, including inability to distinguish isomers and lack of predicted chemical formula annotation.

Purpose of the Study:

  • To develop and validate a data preprocessing workflow to overcome the limitations of existing MS-Cluster tools on the GNPS platform.
  • To improve the accuracy and comprehensiveness of molecular networking analysis for metabolomic datasets.

Main Methods:

  • A novel data preprocessing workflow was developed, integrating MZmine 2 for preliminary data treatment.
  • A custom Python script was created to address specific drawbacks of the MS-Cluster tool, such as isomer differentiation and chemical formula annotation.
  • The workflow was applied to analyze six fractions of varying polarities from a sequential supercritical CO2 extraction of *Stillingia lineata* leaves.

Main Results:

  • The proposed workflow effectively addresses the limitations of MS-Cluster by incorporating retention time data for isomer differentiation.
  • The workflow enables annotation with predicted chemical formulas, enhancing the identification of compounds.
  • Semiquantification is improved beyond simple MS2 scan counts.

Conclusions:

  • The developed data preprocessing workflow significantly enhances the capabilities of molecular networking on the GNPS platform.
  • This approach offers a more robust and accurate method for metabolomic data analysis, particularly for natural product research.
  • The freely available Python script provides a valuable tool for the metabolomic community.