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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...
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...

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Related Experiment Video

Updated: May 24, 2026

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

Accurate mass spectrometry based protein quantification via shared peptides.

Banu Dost1, Nuno Bandeira, Xiangqian Li

  • 1Department of Computer Science and Engineering, UC San Diego, San Diego, California, USA. bdost@ucsd.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|March 15, 2012
PubMed
Summary

Shared peptides, common in mass spectrometry, can now accurately identify and quantify proteins, even those lacking unique peptides. This method improves relative protein abundance measurements and analyzes complex biological systems.

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Last Updated: May 24, 2026

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

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Published on: August 17, 2015

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

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Published on: November 13, 2021

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Mass spectrometry-based protein quantification often discards shared peptides.
  • Shared peptides are ubiquitous in mass spectrometric datasets (~50%).
  • Existing methods struggle with accurate quantification using shared peptides.

Purpose of the Study:

  • To investigate the utility of shared peptides for accurate protein identification and quantification.
  • To develop a method for computing relative protein amounts using shared peptides.
  • To enable the analysis of proteins lacking unique peptides.

Main Methods:

  • Utilized shared peptides for protein quantification.
  • Employed combinatorial optimization to minimize errors in relative abundance measurements.
  • Described topological and numerical properties for robust estimation.

Main Results:

  • Demonstrated that shared peptides can be used to compute relative protein amounts.
  • Showed that proteins without unique peptides can be quantified for relative abundance.
  • Validated the approach through extensive simulations, showing robustness to experimental error.

Conclusions:

  • Shared peptides offer a valuable resource for protein quantification, overcoming limitations of unique peptide-based methods.
  • The developed method enhances the accuracy of relative protein abundance measurements, even in complex biological systems.
  • Applied the method to study host-pathogen interactions in Arabidopsis thaliana, revealing differential protein roles.