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Related Concept Videos

Mass Spectrometry: Branched Alkane Fragmentation01:29

Mass Spectrometry: Branched Alkane Fragmentation

1.6K
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.
1.6K
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

5.3K
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...
5.3K
Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

2.3K
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...
2.3K
Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

3.5K
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...
3.5K
Mass Spectrometry: Cycloalkene Fragmentation00:54

Mass Spectrometry: Cycloalkene Fragmentation

1.5K
The molecular ions of cycloalkenes undergo fragmentation via a retro-Diels–Alder reaction.
1.5K
Mass Spectrometry: Cycloalkane Fragmentation01:05

Mass Spectrometry: Cycloalkane Fragmentation

2.1K
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...
2.1K

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Updated: Jan 8, 2026

Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI
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Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI

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In-Source Fragmentation Annotation in Sterol Mass Spectrometry Imaging.

Iulia Sidorov1,2, Nina Ogrinc1, Lena Spieth3,4,5

  • 1Leiden University Medical Center, Center for Proteomics and Metabolomics, 2333ZA Leiden, The Netherlands.

Analytical Chemistry
|December 18, 2025
PubMed
Summary
This summary is machine-generated.

Mass spectrometry imaging (MSI) using MALDI-2 enhances sterol detection but can cause in-source fragmentation (ISF). This study reveals how ISF complicates cholesterol analysis in spatial biology, highlighting the need for tandem MS to ensure accurate results.

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Area of Science:

  • Spatial biology
  • Molecular imaging
  • Mass spectrometry imaging (MSI)

Background:

  • MSI is crucial for molecular imaging in spatial biology.
  • MALDI-2 technology enhances MSI sensitivity, particularly for neutral metabolites like sterols.
  • Sterols are vital in physiological processes, including neurodegenerative diseases.

Purpose of the Study:

  • Investigate in-source fragmentation (ISF) of cholesterol during MSI.
  • Assess the impact of ISF on biological interpretation under MALDI and MALDI-2 conditions.
  • Introduce a high-resolution MSI technique for precise cholesterol distribution analysis.

Main Methods:

  • Utilized a murine intervention model.
  • Performed MSI under both MALDI and MALDI-2 conditions.
  • Employed high-resolution (5 μm) MSI for spatial analysis.

Main Results:

  • Observed and investigated cholesterol ISF under MALDI and MALDI-2.
  • Demonstrated that ISF can lead to significant misinterpretations in biological analysis.
  • Showcased the utility of high-resolution MSI for precise cholesterol mapping.

Conclusions:

  • ISF is a critical challenge in MSI, potentially compromising accurate molecular annotation.
  • Addressing ISF, especially with MALDI-2, is essential for reliable biological insights.
  • Tandem mass spectrometry is recommended for accurate annotation of in-source fragments.