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Related Concept Videos

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: 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: Amine Fragmentation00:55

Mass Spectrometry: Amine Fragmentation

Amines can be identified using mass spectroscopy based on their characteristic fragmentation patterns. The molecular ions of amines undergo fragmentation via ⍺-cleavage. The ⍺-cleavage of the carbon-carbon bonds in amines generates an alkyl radical and resonance-stabilized nitrogen-containing cation.
In amines, the number of nitrogen atoms affects the mass of the molecular ion, which is described by the nitrogen rule of mass spectrometry. This rule states that a compound containing a single or...

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Related Experiment Video

Updated: Jun 4, 2026

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

A global analysis of peptide fragmentation variability.

Harald Barsnes1, Ingvar Eidhammer, Lennart Martens

  • 1Department of Informatics, University of Bergen, Bergen, Norway.

Proteomics
|February 18, 2011
PubMed
Summary

Analyzing mass spectrometry/mass spectrometry (MS/MS) data reveals significant fragmentation variability, even under controlled conditions. This variability impacts peptide identification and spectral library creation in proteomics research.

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Synthesis and Mass Spectrometry Analysis of Oligo-peptoids
11:44

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Published on: February 21, 2018

Related Experiment Videos

Last Updated: Jun 4, 2026

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids
11:44

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Published on: February 21, 2018

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Mass spectrometry/mass spectrometry (MS/MS) is crucial for peptide identification.
  • Understanding fragmentation patterns is key to validating MS/MS results.
  • Analyzing existing data can improve comprehension of fragmentation processes.

Purpose of the Study:

  • To analyze a large dataset of MS/MS peptide identifications to study fragmentation variability.
  • To investigate variability at the levels of fragment ion detection, rank-based patterns, and general ion occurrence.
  • To discuss findings in the context of spectral library development and predictive software for targeted proteomics.

Main Methods:

  • Analysis of a diverse dataset of MS/MS-based peptide identifications.
  • Examination of peptides identified from multiple spectra on two electrospray instruments.
  • Study of fragmentation variability across three defined levels.

Main Results:

  • Substantial variation in fragment ion detection rates and intensities was observed.
  • Consistency in rank-based fragmentation patterns was limited.
  • General observations revealed variability in fragment ion occurrence irrespective of peptide sequence.
  • Significant variability persists even with high-quality identifications and constant experimental conditions.

Conclusions:

  • Fragmentation variability is a significant factor in MS/MS experiments, even under optimized conditions.
  • This variability poses challenges for creating accurate spectral libraries and developing reliable predictive software for targeted proteomics.
  • Further research is needed to account for and mitigate observed fragmentation inconsistencies.