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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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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: Aromatic Compound Fragmentation01:23

Mass Spectrometry: Aromatic Compound Fragmentation

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...
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: Branched Alkane Fragmentation01:29

Mass Spectrometry: Branched Alkane Fragmentation

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.

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Updated: Jun 5, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Computing fragmentation trees from tandem mass spectrometry data.

Florian Rasche1, Ales Svatos, Ravi Kumar Maddula

  • 1Chair for Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany.

Analytical Chemistry
|December 25, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for interpreting mass spectrometry data by computing fragmentation trees. This approach aids in identifying unknown organic compounds by analyzing their structure and dependencies, even without a spectral database.

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High-resolution Tandem Mass Spectrometry for Studying Chemical Constituents of Gynura bicolor DC
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High-resolution Tandem Mass Spectrometry for Studying Chemical Constituents of Gynura bicolor DC

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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High-resolution Tandem Mass Spectrometry for Studying Chemical Constituents of Gynura bicolor DC
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High-resolution Tandem Mass Spectrometry for Studying Chemical Constituents of Gynura bicolor DC

Published on: February 2, 2024

Area of Science:

  • Analytical Chemistry
  • Computational Chemistry
  • Biochemistry

Background:

  • Structural elucidation of organic compounds in complex biological samples is a major analytical challenge.
  • Manual interpretation of collision-induced dissociation (CID) mass spectra is time-consuming and requires specialized expertise.
  • Current automated compound identification relies heavily on spectral library matching, limiting the analysis of unknown compounds.

Purpose of the Study:

  • To develop a novel computational method for interpreting CID mass spectra of protonated organic ions.
  • To enable the automated identification of unknown organic compounds by analyzing their fragmentation patterns.
  • To advance the field of mass spectrometry-based structural elucidation.

Main Methods:

  • Computing fragmentation trees to model ion dissociation pathways.
  • Establishing molecular formulas and dependencies between fragment ions.
  • Applying the method to interpret CID spectra of organic compounds.

Main Results:

  • The developed method successfully interprets CID spectra by generating fragmentation trees.
  • It determines the molecular formula of the parent compound and all fragment ions.
  • The method elucidates the dependencies between fragment ions, offering deeper structural insights.

Conclusions:

  • This fragmentation tree computation method represents a significant advancement in interpreting CID mass spectra.
  • It facilitates the automated identification of unknown organic compounds not present in existing spectral databases.
  • The approach holds promise for enhancing structural elucidation in complex biological matrices.