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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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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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...
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Related Experiment Video

Updated: Apr 11, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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MS(3)-based quantitative proteomics using pulsed-Q dissociation.

Zhiyun Cao1, Adam R Evans1, Renã A S Robinson1

  • 1Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA.

Rapid Communications in Mass Spectrometry : RCM
|June 6, 2015
PubMed
Summary
This summary is machine-generated.

Pulsed-Q dissociation (PQD)-MS(3) enhances isobaric tagging accuracy in mass spectrometry. This method improves protein quantification and identification, offering a valuable tool for proteomic analysis.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Analytical Chemistry

Background:

  • Isobaric tagging reagents like TMT and iTRAQ enable high-throughput proteomic analysis.
  • Limitations in MS/MS accuracy arise from co-isolation and co-fragmentation, affecting quantification.
  • A novel MS(3) method using pulsed-Q dissociation (PQD) is proposed to address these limitations.

Purpose of the Study:

  • To evaluate the efficacy of PQD-MS(3) for improving accuracy and precision in isobaric tag-based quantitative proteomics.
  • To compare PQD-MS(3) with traditional HCD-MS(3) methods in terms of protein identification and quantification.
  • To demonstrate the applicability of PQD-MS(3) across different mass spectrometry instruments.

Main Methods:

  • Mouse brain protein digests were labeled with TMT reagents and mixed in specific molar ratios.
  • Analysis was performed using both HCD-MS(3) and PQD-MS(3) methods.
  • MS(3) acquisition involved selecting either the most intense fragment ion or the y1 ion for further fragmentation.

Main Results:

  • PQD-MS(3) methods yielded accurate protein ratios comparable to HCD-MS(3).
  • PQD-MS(3) significantly increased the number of identified and quantified proteins and peptide spectral counts.
  • Both top ion and y1 ion strategies in PQD-MS(3) demonstrated improved performance.

Conclusions:

  • PQD-MS(3) is an effective strategy to improve data quality in isobaric tag quantitative proteomics.
  • The method enhances MS/MS spectra collection and increases the number of quantified proteins.
  • PQD-MS(3) is compatible with both Orbitrap and ion trap mass spectrometers, broadening its accessibility.