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

3.9K
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...
3.9K
Mass Spectrometry: Cycloalkene Fragmentation00:54

Mass Spectrometry: Cycloalkene Fragmentation

1.2K
The molecular ions of cycloalkenes undergo fragmentation via a retro-Diels–Alder reaction.
1.2K
Mass Spectrometry: Cycloalkane Fragmentation01:05

Mass Spectrometry: Cycloalkane Fragmentation

1.6K
In mass spectrometry, cycloalkanes exhibit distinct fragmentation patterns due to the inherent stability of their molecular ions compared to linear or branched alkanes. The ring structure of cycloalkanes provides additional stability to the molecular ions, often resulting in prominent ion peaks in the mass spectrum.
For example, cyclohexane molecular ions have a mass-to-charge ratio (m/z) of 84, which tends to produce a stronger signal than linear alkanes like hexane. This stability comes from...
1.6K
Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

2.9K
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...
2.9K
Mass Spectrometry: Branched Alkane Fragmentation01:29

Mass Spectrometry: Branched Alkane Fragmentation

1.2K
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.
1.2K
Mass Spectrometry: Alkyne Fragmentation00:53

Mass Spectrometry: Alkyne Fragmentation

1.7K
The fragmentation of alkynes preferentially occurs at the carbon–carbon bond between the α and β carbon of the alkyne bond to generate a 3-propynyl cation (or propargyl cation). In terminal alkynes, there is the only type of fragmentation that yields the 3-propynyl cation. The unsubstituted 3-propynyl cation exhibits a peak at a mass-to-charge ratio of 39. In internal alkynes, the 3-propynyl cation is substituted. For example, 2-pentyne fragments into methyl-substituted...
1.7K

You might also read

Related Articles

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

Sort by
Same author

Mycobacteria Amplicon Sequencing Tool: automated resistance prediction and lineage classification for <i>Mycobacterium tuberculosis</i>.

Microbiology resource announcements·2026
Same author

Antitarget profiling of mycotoxins via molecular docking.

Molecular diversity·2026
Same author

Turnover Rate of Lipids, Metabolites and Proteins Revealed by 156-Day-Long D<sub>2</sub>O Administration in a Guinea Pig.

International journal of molecular sciences·2026
Same author

Physicochemical and Toxicological Characterization of Airborne Brake Wear Particles Reveals Oxidative Stress-Mediated DNA Damage.

Environmental science & technology·2026
Same author

Towards Explainable Computational Toxicology: Linking Antitargets to Rodent Acute Toxicity.

Pharmaceutics·2025
Same author

Exposures in Indoor Air Affecting Health.

Allergy·2025

Related Experiment Video

Updated: Sep 28, 2025

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
06:29

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Published on: March 3, 2021

5.7K

PyFragMS-A Web Tool for the Investigation of the Collision-Induced Fragmentation Pathways.

Yury Kostyukevich1, Sergey Sosnin1, Sergey Osipenko1

  • 1Skolkovo Institute of Science and Technology, Novaya Street, 100, Skolkovo 143025, Russian Federation.

ACS Omega
|March 30, 2022
PubMed
Summary

Understanding molecule fragmentation in mass spectrometry is crucial. This study introduces PyFragMS, a tool using fragmentation trees and labeled compounds to clarify how protonation sites affect fragmentation pathways.

More Related Videos

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
08:35

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

5.9K
Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers
08:51

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers

Published on: August 18, 2017

10.5K

Related Experiment Videos

Last Updated: Sep 28, 2025

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
06:29

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Published on: March 3, 2021

5.7K
Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
08:35

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

5.9K
Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers
08:51

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers

Published on: August 18, 2017

10.5K

Area of Science:

  • Analytical Chemistry
  • Computational Chemistry
  • Spectroscopy

Background:

  • Tandem mass spectrometry (MS/MS) is vital for identifying molecules via fragmentation.
  • Existing databases and in silico prediction tools for MS/MS spectra have limitations.
  • Fragmentation mechanisms are not fully understood, especially how different protonation sites (protomers) affect spectra.

Purpose of the Study:

  • To develop a novel approach for understanding mass spectrometry fragmentation.
  • To investigate the influence of protonation site on fragmentation pathways.
  • To enhance the accuracy of molecular identification using MS/MS data.

Main Methods:

  • Developed PyFragMS, a web tool integrating a database of annotated MS/MS spectra of isotopically labeled molecules (H/D, 16O/18O exchange).
  • Implemented computational tools for generating fragmentation trees, which map all consecutive fragmentation events.
  • Utilized MS/MS data from isotopically labeled compounds to analyze fragmentation patterns.

Main Results:

  • Demonstrated how PyFragMS can elucidate the impact of protonation site on small molecule fragmentation pathways.
  • Showcased the capability of PyFragMS to perform database searches incorporating MS/MS data from labeled compounds.
  • Provided a more detailed understanding of fragmentation mechanisms by analyzing fragmentation trees.

Conclusions:

  • PyFragMS offers a powerful combined approach of fragmentation trees and isotopically labeled MS/MS data.
  • The tool aids in resolving ambiguities caused by overlapping spectra from different protomers.
  • This method advances the identification of small molecules in mass spectrometry.