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Related Concept Videos

Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

6.1K
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...
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Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

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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...
2.8K
Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

3.9K
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...
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Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

3.8K
An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
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Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

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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...
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Mass Spectrometry: Aldehyde and Ketone Fragmentation01:09

Mass Spectrometry: Aldehyde and Ketone Fragmentation

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In mass spectrometry, the fragmentation of aliphatic aldehydes and ketones generally occurs through three key mechanisms: α-cleavage, inductive cleavage, and the McLafferty rearrangement.
5.1K

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Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software.

Hiroshi Tsugawa1, Tobias Kind2, Ryo Nakabayashi1

  • 1RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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We developed nine rules for hydrogen rearrangement in mass spectrometry to improve compound identification. Our MS-FINDER software accurately predicts molecular formulas and structures from MS/MS spectra, aiding untargeted metabolomics research.

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Area of Science:

  • Metabolomics
  • Computational Chemistry
  • Mass Spectrometry

Background:

  • Compound identification from accurate mass MS/MS spectra is a significant bottleneck in untargeted metabolomics.
  • Existing methods struggle with the complexity of fragmentation patterns and hydrogen rearrangements.

Purpose of the Study:

  • To propose nine rules for hydrogen rearrangement (HR) during low-energy collision-induced dissociation (CID) fragmentation.
  • To develop and validate the MS-FINDER software for in silico MS/MS fragmentation prediction and structure elucidation.

Main Methods:

  • Formulated nine HR rules based on the even-electron rule, covering heteroatoms and multistage fragmentation.
  • Evaluated HR rules using MassBank and GNPS MS/MS spectral databases and enthalpy calculations.
  • Developed MS-FINDER to predict molecular formulas and rank isomers using bond dissociation energies, mass accuracies, fragment linkages, and HR rules.

Main Results:

  • 78.4% of MassBank and 84.8% of GNPS MS/MS fragment ions were resolved using the HR rules.
  • MS-FINDER achieved 98.0% accuracy in predicting molecular formulas for MassBank records.
  • MS-FINDER identified the correct structural isomer within the top-3 candidates with 82.1% accuracy for MassBank and 80.4% for human plasma data.

Conclusions:

  • The proposed HR rules effectively explain and predict MS/MS fragmentation patterns.
  • MS-FINDER significantly improves the accuracy and efficiency of compound identification in untargeted metabolomics.
  • The software provides a valuable tool for structure elucidation, even for compounds not present in spectral libraries.