Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Experimental Determination of Chemical Formula

Experimental Determination of Chemical Formula

The elemental makeup of a compound defines its chemical identity, and chemical formulas are the most concise way of representing this elemental makeup. When a compound’s formula is unknown, measuring the mass of its constituent elements is often the first step in determining the formula experimentally.

MO Theory and Covalent Bonding

MO Theory and Covalent Bonding

The molecular orbital theory describes the distribution of electrons in molecules in a manner similar to the distribution of electrons in atomic orbitals. The region of space in which a valence electron in a molecule is likely to be found is called a molecular orbital. Mathematically, the linear combination of atomic orbitals (LCAO) generates molecular orbitals. Combinations of in-phase atomic orbital wave functions result in regions with a high probability of electron density, while...

Molecular Shapes

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...

Polymers: Molecular Weight Distribution

Polymers: Molecular Weight Distribution

For any given polymer, the weight average molecular weight (Mw) is higher than, if not equal to, the number average molecular weight (Mn). The only situation in which the weight average molecular weight and the number average molecular weight are equal is when a polymer consists only of chains with equal molecular weight. However, this never happens in a synthetic polymer, since it is difficult to control the polymerization process up to a molecular level with accuracy to a hundred percent.

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

You might also read

Related Articles

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

Sort by

Same author

Comparative genomic analysis of <i>Bacteroides fragilis</i> from intestinal and extra-intestinal sites.

Microbiology spectrum·2026

Same author

Exosomal Profiling Reveals Mechanisms of Hibernation-Associated Neuroprotection.

bioRxiv : the preprint server for biology·2026

Same author

Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data.

bioRxiv : the preprint server for biology·2026

Same author

MALDI Tandem Mass Spectrometry for Colony-Based Dereplication of Natural Products.

bioRxiv : the preprint server for biology·2026

Same author

Large-scale discovery platform enables identification of peptides targeting drug-resistant candidiasis.

Cell reports methods·2026

Same author

Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles.

Gut microbes·2026

Search research articles

Related Experiment Video

Updated: Oct 19, 2025

Author Spotlight: Characterization of Low-Affinity Protein Interactions in Solution Using MassFluidix Technology

Author Spotlight: Characterization of Low-Affinity Protein Interactions in Solution Using MassFluidix Technology

Published on: January 26, 2024

Chemical Proportionality within Molecular Networks.

Daniel Petras^1,2,3, Andrés Mauricio Caraballo-Rodríguez^1,2, Alan K Jarmusch^1,2

¹Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, California 92093, United States.

Analytical Chemistry

|September 17, 2021

Summary

Chemical Proportionality (ChemProp) contextualizes molecular networks by scoring abundance changes between connected molecules. This method prioritizes biologically relevant transformations and proportional changes in related compounds within complex datasets.

More Related Videos

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

Related Experiment Videos

Last Updated: Oct 19, 2025

Author Spotlight: Characterization of Low-Affinity Protein Interactions in Solution Using MassFluidix Technology

Author Spotlight: Characterization of Low-Affinity Protein Interactions in Solution Using MassFluidix Technology

Published on: January 26, 2024

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

Area of Science:

Computational chemistry
Bioinformatics
Analytical chemistry

Background:

Molecular networking connects structurally similar molecules using mass spectrometry fragmentation data.
Analyzing dynamic changes in molecular abundance within networks is crucial for understanding biological and chemical processes.

Purpose of the Study:

To introduce Chemical Proportionality (ChemProp) for contextualizing molecular networks.
To develop a method for scoring and visualizing abundance changes between connected molecules in sequential data.
To prioritize molecules and transformations in biological and chemical systems.

Main Methods:

Developed the ChemProp workflow to score abundance variations between nodes in molecular networks.
Applied ChemProp to sequential data series, such as temporal or spatial relationships.
Utilized Global Natural Products Social Molecular Networking (GNPS) for workflow implementation.

Main Results:

ChemProp successfully contextualized molecular networks by scoring abundance changes.
The workflow demonstrated utility in prioritizing specific molecules in various biological contexts.
Demonstrated application in bacterial bile acid transformations, human drug metabolism, and natural product biosynthesis.

Conclusions:

ChemProp provides a novel approach to analyze and interpret molecular networks based on abundance dynamics.
The tool enhances the prioritization of key molecules and transformations in complex biological systems.
ChemProp is freely accessible via the GNPS environment, promoting broader research applications.