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Related Concept Videos

Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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...
Effects of EDTA on End-Point Detection Methods01:18

Effects of EDTA on End-Point Detection Methods

Different methods, such as visual observance of metal-ion indicators, spectroscopic techniques, and potentiometric methods, can determine the endpoint of an EDTA titration.
In the visual method, metal-ion indicators (metallochromic dyes), which have distinct colors in their free and complex forms, are added to the mixture to signal the titration's end point. They form stable complexes with metal ions, but these complexes are weaker than the corresponding metal–EDTA complexes. As a result, EDTA...
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 Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation01:01

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

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 fragmentation of...
Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

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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Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay
06:17

Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay

Published on: February 28, 2025

ETD fragmentation features improve algorithm.

Wenzhou Li1, Vicki H Wysocki

  • 1Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.

Expert Review of Proteomics
|July 20, 2012
PubMed
Summary
This summary is machine-generated.

Improving peptide identification in mass spectrometry is crucial. A new method removes specific peaks in electron transfer dissociation (ETD) data, enhancing protein identification accuracy with algorithms like OMSSA.

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Last Updated: May 20, 2026

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Published on: February 28, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
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Published on: May 29, 2021

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09:19

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioanalytical Chemistry

Background:

  • Electron transfer dissociation (ETD) is an emerging mass spectrometry technique for proteomics.
  • Current protein identification algorithms often fail to leverage unique ETD spectral features.
  • Existing algorithms are typically derived from collision-activated dissociation (CAD) methods.

Discussion:

  • Sridhara and colleagues developed a method to improve ETD peptide identification.
  • The technique involves removing charge-reduced precursors and neutral loss peaks from ETD spectra.
  • These specific peaks are critical for accurate peptide identification and precursor charge determination in low-resolution data.

Key Insights:

  • Successfully enhancing protein identification rates using ETD data.
  • Demonstrating the utility of incorporating ETD-specific fragmentation characteristics into algorithms.
  • Providing a practical example of algorithm refinement for a newer mass spectrometry technique.

Outlook:

  • Potential for broader application of this method in proteomics research.
  • Further development of ETD-specific algorithms to maximize proteomic data utility.
  • Improved accuracy in mass spectrometry-based protein identification through tailored algorithmic approaches.