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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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Updated: Jun 16, 2026

Quantitative Analysis of Chromatin Proteomes in Disease
08:11

Quantitative Analysis of Chromatin Proteomes in Disease

Published on: December 28, 2012

Role of spectral counting in quantitative proteomics.

Deborah H Lundgren1, Sun-Il Hwang, Linfeng Wu

  • 1Department of Cell Biology and Center for Vascular Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA.

Expert Review of Proteomics
|February 4, 2010
PubMed
Summary

Spectral counting is a widely used method for measuring protein abundance in proteomic studies. This review examines its performance, limitations, and statistical analysis challenges, particularly in estimating false discovery rates.

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Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
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Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

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Last Updated: Jun 16, 2026

Quantitative Analysis of Chromatin Proteomes in Disease
08:11

Quantitative Analysis of Chromatin Proteomes in Disease

Published on: December 28, 2012

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

Area of Science:

  • Proteomics
  • Biochemistry
  • Bioinformatics

Background:

  • Spectral counting is a common label-free, semiquantitative technique for assessing protein abundance in proteomic research.
  • Its practical application in determining protein levels has become widely accepted.

Purpose of the Study:

  • To critically review the performance and limitations of spectral counting in quantitative proteomics.
  • To explore the impact of data modifications on abundance estimations.
  • To compare various statistical methods used in spectral count analysis.

Main Methods:

  • Review of existing literature on spectral counting methodologies.
  • Analysis of statistical frameworks applied to spectral count data.
  • Critique of different quantitation study designs utilizing spectral counting.

Main Results:

  • Identified challenges in spectral counting performance relative to other label-free methods.
  • Evaluated the consequences of common modifications to raw spectral counts.
  • Compared diverse statistical approaches for spectral count analysis, highlighting areas of concern.

Conclusions:

  • Spectral counting offers a practical approach to protein quantitation but has inherent limitations.
  • Accurate statistical analysis and false discovery rate estimation remain significant challenges in quantitative proteomics.
  • Further research is needed to refine methodologies for robust protein abundance determination.