Related Experiment Video
Updated: Feb 11, 2026
08:09
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
20.6K
Propagating annotations of molecular networks using in silico fragmentation
Ricardo R da Silva1,2, Mingxun Wang1, Louis-Félix Nothias1
1Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America.
Plos Computational Biology
|April 19, 2018
Summary
This study introduces a new method to improve small molecule identification in mass spectrometry. Molecular networking enhances in silico predictions, increasing annotation accuracy even without spectral library matches.
Area of Science:
- Analytical Chemistry
- Metabolomics
- Computational Chemistry
Background:
- Small molecule annotation is crucial for biological interpretation in untargeted mass spectrometry.
- Molecular networking organizes MS/MS data, but annotation propagation typically requires manual spectral inspection and library matches.
- In silico predictions offer an alternative but face challenges with structural candidate uncertainty.
Purpose of the Study:
- To enhance the accuracy of in silico small molecule structure predictions using molecular networking.
- To develop a method for propagating structural annotations in molecular networks, even without spectral library data.
Main Methods:
- Utilizing molecular network topology and structural similarity to create a network consensus.
- Re-ranking in silico predicted structural candidates based on network information.
- Implementing the Network Annotation Propagation (NAP) tool within the GNPS web-platform.
Main Results:
- Demonstrated improved accuracy of in silico predictions through network-based annotation propagation.
- Successfully propagated structural annotations without relying on spectral library matches.
- Developed the NAP tool to integrate molecular networking with in silico annotation.
Conclusions:
- Molecular networking can significantly improve the reliability of in silico small molecule annotations.
- The NAP tool provides a novel approach to address uncertainties in in silico predictions for mass spectrometry.
- This method advances the field of untargeted metabolomics by enabling more accurate structural identifications.
Related Concept Videos
01:20Mass Spectrometry: Molecular Fragmentation Overview
5.8K
The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
5.8K
02:31Habitat Fragmentation
21.5K
Habitat fragmentation describes the division of a more extensive, continuous habitat into smaller, discontinuous areas. Human activities such as land conversion, as well as slower geological processes leading to changes in the physical environment, are the two leading causes of habitat fragmentation. The fragmentation process typically follows the same steps: perforation, dissection, fragmentation, shrinkage, and attrition.
21.5K
02:26Protein Networks
4.6K
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,...
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,...
4.6K
03:36Genome Annotation and Assembly
21.1K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.1K
01:07Propagation of Waves
3.0K
When a wave propagates from one medium to another, part of it may get reflected in the first medium, and part of it may get transmitted to the second medium. In such a case, the interface of the two mediums can be considered as a boundary that is neither fixed nor free.
Consider a scenario where a wave propagates from a string of low linear mass density to a string of high linear mass density. In such a case, the reflected wave is out of phase with respect to the incident wave, however the...
Consider a scenario where a wave propagates from a string of low linear mass density to a string of high linear mass density. In such a case, the reflected wave is out of phase with respect to the incident wave, however the...
3.0K
02:18Network Covalent Solids
16.2K
Network covalent solids contain a three-dimensional network of covalently bonded atoms as found in the crystal structures of nonmetals like diamond, graphite, silicon, and some covalent compounds, such as silicon dioxide (sand) and silicon carbide (carborundum, the abrasive on sandpaper). Many minerals have networks of covalent bonds.
To break or to melt a covalent network solid, covalent bonds must be broken. Because covalent bonds are relatively strong, covalent network solids are typically...
To break or to melt a covalent network solid, covalent bonds must be broken. Because covalent bonds are relatively strong, covalent network solids are typically...
16.2K