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Related Concept Videos

Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

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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...
5.2K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

2.1K
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
2.1K
Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

2.2K
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...
2.2K
Mass Spectrometry: Aromatic Compound Fragmentation01:23

Mass Spectrometry: Aromatic Compound Fragmentation

2.3K
Upon ionization, aromatic compounds generate a molecular ion that is observed as a prominent peak in their mass spectra. For example, the molecular ion peak for benzene appears at a mass-to-charge ratio of 78, while toluene is observed at a mass-to-charge ratio of 92. The molecular ion benzene is highly stable and does not readily undergo further fragmentation due to the significant amount of energy required to disrupt the aromatic stability of the benzene ring. In contrast, the molecular ion...
2.3K
Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

2.2K
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...
2.2K
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

2.5K
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...
2.5K

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A Frequency-Based Approach to Predict the Low-Energy Collision-Induced Dissociation Fragmentation Spectra.

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A new method accurately predicts peptide tandem mass spectra using fragmentation statistics. This advance improves peptide identification in high-throughput proteomics research by correlating better with experimental data than existing tools.

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Area of Science:

  • Proteomics
  • Computational Biology
  • Mass Spectrometry

Background:

  • Peptide identification in tandem mass spectrometry relies on comparing experimental and theoretical spectra.
  • Accurate theoretical spectrum prediction is crucial for high-throughput proteomics.
  • Understanding peptide fragmentation is key to improving prediction accuracy.

Purpose of the Study:

  • To develop a novel method for predicting theoretical ion trap collision-induced dissociation (CID) tandem mass spectra.
  • To predict spectra for singly, doubly, and triply charged tryptic peptides.
  • To enhance peptide identification accuracy in proteomics.

Main Methods:

  • Utilized fragmentation statistics from ion trap CID spectra.
  • Estimated relative cleavage frequencies for adjacent amino acid pairs.
  • Developed a prediction method based on cleavage frequencies.

Main Results:

  • The novel method achieved high correlation between predicted and experimental spectra (99.73% > 0.8 correlation).
  • The new method significantly outperformed existing tools (OpenMS_Simulator, MS2PIP, MS2PBPI).
  • Cleavage frequency directly predicts tandem mass spectra effectively.

Conclusions:

  • The developed method provides accurate theoretical tandem mass spectra prediction.
  • This approach offers a significant improvement over current spectrum prediction tools.
  • The findings facilitate more reliable peptide identification in proteomics.