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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...

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Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
09:04

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

Peptide and protein quantification using iTRAQ with electron transfer dissociation.

Doug Phanstiel1, Yi Zhang, Jarrod A Marto

  • 1Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Journal of the American Society for Mass Spectrometry
|July 16, 2008
PubMed
Summary
This summary is machine-generated.

Electron transfer dissociation (ETD) is compatible with isobaric tags for relative and absolute quantification (iTRAQ) labeling for peptide quantification. ETD offers reliable quantification, comparable to other methods, especially for high-intensity reporter ions in proteomic analyses.

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Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry
06:09

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Published on: July 31, 2011

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Analytical Chemistry

Background:

  • Electron transfer dissociation (ETD) is a peptide fragmentation technique valuable for sequencing peptides with post-translational modifications (PTMs).
  • Isobaric tags for relative and absolute quantification (iTRAQ) is a common method for quantitative proteomics.
  • Compatibility of ETD with iTRAQ labeling for quantification was previously undetermined due to differing fragmentation mechanisms.

Purpose of the Study:

  • To investigate the compatibility of ETD with iTRAQ labeling for peptide and protein quantification.
  • To characterize the fragmentation patterns of ETD on iTRAQ-labeled peptides.
  • To compare the quantification performance of ETD with other dissociation methods like collision-activated dissociation (CAD).

Main Methods:

  • ETD fragmentation of iTRAQ-labeled synthetic peptides.
  • High mass accuracy Orbitrap mass analysis to determine product ion formulas.
  • Quantification of peptides and proteins using iTRAQ labeling in conjunction with ETD, beam-type CAD, and pulsed Q dissociation (PQD) on a hybrid ion trap-Orbitrap mass spectrometer.

Main Results:

  • ETD of iTRAQ-labeled peptides produces unique c- and z-type fragment ions and reporter ions.
  • ETD cleavage of the iTRAQ tag yields quantifiable fragment ions, supporting up to three channels of quantification with quality similar to beam-type CAD.
  • Reliable peptide quantification (average error <10%) was achieved with ETD, beam-type CAD, and PQD for reporter ion intensities above a threshold.
  • ETD, HCD, and PQD had 36%, 8%, and 16% of scans below the quantification threshold, respectively.
  • Average protein-level errors were 2.3% for ETD, 1.7% for HCD, and 3.6% for PQD.

Conclusions:

  • ETD is a viable fragmentation technique for quantitative proteomic analyses using iTRAQ labeling.
  • ETD provides reliable peptide and protein quantification, comparable to established methods, particularly for high-intensity signals.
  • The unique fragmentation patterns of ETD on iTRAQ-labeled peptides enable accurate quantitative measurements in complex proteomic samples.