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

Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

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...
Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

Alkenes lose one electron from the unsaturated π bond upon ionization and form stable molecular ions. Further fragmentation of alkenes occurs through three different reaction pathways. The most prominent fragmentation is the cleavage at the allylic position. The resultant allylic carbocation is resonance stabilized. In the mass spectra of terminal alkenes, this fragment appears at a mass-to-charge ratio of 41. In the internal alkenes, where there are two choices of allylic cleavage, the...
Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

The molecular ions of linear alkanes prefer to fragment at the carbon-carbon bond away from the end of the chain since the cleavage of an inner bond creates a stable carbocation and a stable radical. Consequently, the mass signals of linear alkanes feature intense peaks in the middle of the mass-to-charge ratio plot with weaker peaks on either end. The fragmentation of each carbon-carbon bond with the release of a methyl group in each splitting leads to prominent peaks in the mass spectra...
Mass Spectrometry: Branched Alkane Fragmentation01:29

Mass Spectrometry: Branched Alkane Fragmentation

This lesson delves into the mass spectrometry of branched alkane fragmentation. Branched alkanes possess secondary or tertiary carbon atoms, which generate relatively stable carbocations if the cleavage occurs at the branching point. The high stability of carbocations drives the instant fragmentation of branched alkanes. Accordingly, the branched alkane's molecular ion peak is very weak or invisible in the mass spectra, especially in comparison to a linear alkane.
Mass Spectrometry: Alcohol Fragmentation01:03

Mass Spectrometry: Alcohol Fragmentation

Alcohols (R-OH) ionize to lose one non-bonded electron from the oxygen atom, forming molecular ions. Due to their tendency to fragment rapidly, the intensity of the molecular ion peak in the mass spectrum is weak or sometimes absent. The fragmentation patterns for alcohols occur in two ways, i.e. ⍺-cleavage and dehydration. During ⍺-cleavage, the bond at the ⍺-position adjacent to the hydroxyl group cleaves to give a resonance-stabilized cation and a radical. However, intramolecular dehydration...
Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

The fragmentation patterns observed for compounds such as carboxylic acids, esters, and amides in the mass spectra include ⍺-cleavage and McLafferty rearrangement. Fragmentation by ⍺-cleavage preferentially occurs at the carbon-carbon bond at the ⍺-position next to the carboxylic group to generate a neutral radical and a cation. Long chain compounds with hydrogen at their γ-carbon undergo McLafferty rearrangement to give a radical cation and a neutral alkene.
For example, the fragmentation of...

You might also read

Related Articles

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

Sort by
Same author

Sickle Cell Disease and Kidney Injury: Circulating Uromodulin Allows Early Tissue Specific Diagnosis and Monitoring of Treatment.

American journal of hematology·2026
Same author

High-risk and low-risk human papillomavirus detection in self-collected samples compared to clinician-collected samples in a Polish population.

Frontiers in public health·2026
Same author

SHACLens: a visualization workflow for SHACL violation exploration in knowledge graphs.

Frontiers in bioinformatics·2026
Same author

Finding the most promising indications for novel treatments in oncology.

NPJ precision oncology·2026
Same author

Prevalence of celiac disease in a Tunisian cohort.

Frontiers in gastroenterology (Lausanne, Switzerland)·2026
Same author

Integration of palladium-catalyzed C-N coupling into self-encoded libraries for accelerated hit discovery.

RSC chemical biology·2026
Same journal

Machine Learning-Assisted Label-Free SERS Decoding of Mitochondrial Molecular Dynamics in Ovarian Granulosa Cells during Aging.

Analytical chemistry·2026
Same journal

Revealing the Regulatory Interplay of NHE1 mRNA and Na<sup>+</sup> in Cancer Cells Using a DNA Nanosensor.

Analytical chemistry·2026
Same journal

Towards Cellular Resolution of Tryptic Peptides in Tissue Sections by MALDI MS Imaging: A Focus on Enzyme Application and Reproducibility.

Analytical chemistry·2026
Same journal

Bioinspired Bilayer Hydrogel Colorimetric Sensor Array for Low-Temperature Food Freshness Analysis.

Analytical chemistry·2026
Same journal

Quartz Crystal Microbalance-Based Point-of-Care Testing Systems: Principles, Device Design, and Applications.

Analytical chemistry·2026
Same journal

Heterojunction Gate-Empowered OPECT Aptasensing: A Valid Protocol for Realizing High Current Gain at Low Electron Donor Dependency.

Analytical chemistry·2026
See all related articles

Related Experiment Video

Updated: May 24, 2026

Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay
06:17

Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay

Published on: February 28, 2025

Identifying the unknowns by aligning fragmentation trees.

Florian Rasche1, Kerstin Scheubert, Franziska Hufsky

  • 1Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany.

Analytical Chemistry
|March 7, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces automated fragmentation tree alignment for comparing small molecule mass spectrometry data. This method accurately clusters compounds and identifies unknown molecules, even those not in existing databases.

More Related Videos

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery
06:26

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Published on: May 16, 2021

Related Experiment Videos

Last Updated: May 24, 2026

Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay
06:17

Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay

Published on: February 28, 2025

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery
06:26

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Published on: May 16, 2021

Area of Science:

  • Analytical Chemistry
  • Computational Chemistry
  • Metabolomics

Background:

  • Mass spectrometry (MS) is crucial for analyzing small molecules.
  • Tandem mass spectrometry (MS/MS) can identify unknown compounds but automated interpretation is challenging.
  • Fragmentation trees offer a novel approach to analyzing MS/MS data.

Purpose of the Study:

  • To develop an automated method for comparing small molecule fragmentation patterns using fragmentation trees.
  • To cluster compounds based on fragmentation patterns and assess correlation with chemical similarity.
  • To create a tool for searching databases and identifying unknown small molecules.

Main Methods:

  • Automated comparison of fragmentation patterns by aligning fragmentation trees.
  • Clustering compounds based solely on fragmentation pattern similarity.
  • Development of a search tool for comparing unknown sample fragmentation patterns against a database.
  • Application of the method to identify metabolites in Icelandic poppy.

Main Results:

  • Clustering based on fragmentation patterns showed good agreement with known compound classes.
  • Fragmentation pattern similarity strongly correlated with chemical similarity between molecules.
  • The developed tool successfully identified unknown small molecules from Icelandic poppy metabolites.
  • The method enables fully automated computational identification of novel small molecules.

Conclusions:

  • Automated fragmentation tree alignment is effective for comparing and clustering small molecules.
  • This approach significantly advances the automated interpretation of tandem mass spectrometry data.
  • The developed tool has practical applications in metabolomics and drug discovery for identifying unknown compounds.