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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: 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 Analyzers: Overview01:13

Mass Analyzers: Overview

The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
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: Cycloalkane Fragmentation01:05

Mass Spectrometry: Cycloalkane Fragmentation

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

Mass Spectrometry: Aldehyde and Ketone Fragmentation

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

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Natural Product Discovery with LC-MS/MS Diagnostic Fragmentation Filtering: Application for Microcystin Analysis
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Natural Product Discovery with LC-MS/MS Diagnostic Fragmentation Filtering: Application for Microcystin Analysis

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FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data.

Harald Barsnes1, Ingvar Eidhammer, Lennart Martens

  • 1Department of Informatics, University of Bergen, Bergen, Norway. Harald.Barsnes@ii.uib.no

Proteomics
|January 6, 2010
PubMed
Summary
This summary is machine-generated.

FragmentationAnalyzer is a free tool for analyzing large MS/MS data sets. It helps assess peptide and protein identifications by detecting fragmentation pattern nuances related to instruments or post-translational modifications.

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

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Last Updated: Jun 17, 2026

Natural Product Discovery with LC-MS/MS Diagnostic Fragmentation Filtering: Application for Microcystin Analysis
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Natural Product Discovery with LC-MS/MS Diagnostic Fragmentation Filtering: Application for Microcystin Analysis

Published on: May 31, 2019

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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
09:19

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

Area of Science:

  • Mass spectrometry
  • Proteomics
  • Bioinformatics

Background:

  • Understanding peptide fragmentation in tandem mass spectrometry (MS/MS) is crucial for accurate peptide and protein identification.
  • Variations in fragmentation patterns can arise from specific instruments or the presence of post-translational modifications (PTMs).

Purpose of the Study:

  • To introduce FragmentationAnalyzer, a freely available, open-source software tool.
  • To enable straightforward analysis of large MS/MS datasets for specific peptide types.
  • To facilitate the detection of fragmentation pattern nuances.

Main Methods:

  • Development of the open-source FragmentationAnalyzer tool.
  • Utilizing a common set of peptide properties for analysis.
  • Analysis of large-scale MS/MS data.

Main Results:

  • FragmentationAnalyzer simplifies the analysis of MS/MS data.
  • The tool allows for the detection of subtle fragmentation differences.
  • Identified nuances can be linked to specific mass spectrometry instruments or PTMs.

Conclusions:

  • FragmentationAnalyzer is a valuable tool for researchers in proteomics and bioinformatics.
  • The tool enhances the assessment of peptide and protein identifications from MS/MS data.
  • It aids in understanding the impact of experimental variables on fragmentation patterns.