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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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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.
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Two-dimensional gel electrophoresis is a high-resolution protein separation method first introduced by O' Farrell and Klose in 1975. This method involves protein separation by two dimensions, mass and charge, making it more accurate than one-dimensional gel electrophoresis.
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Updated: Mar 29, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Multiple Testing and Pattern Recognition in 2-DE Proteomics.

Sebastien C Carpentier1,2

  • 1Department of Biosystems, Faculty of Bioscience Engineering, K.U. Leuven, Willem Decroylaan 42, Leuven, 3001, Belgium. sebastien.carpentier@biw.kuleuven.be.

Methods in Molecular Biology (Clifton, N.J.)
|November 28, 2015
PubMed
Summary
This summary is machine-generated.

Two-dimensional gel electrophoresis (2-DE) remains valuable for quantifying protein abundances, especially for studying genetic variations, alternative splicing, and post-translational modifications (PTMs). This review offers statistical tools and guidelines for discovering and characterizing protein spots and their PTMs.

Keywords:
2-DEClusteringMultivariate statisticsProtein correlationsProtein isoforms

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Area of Science:

  • Proteomics
  • Biochemistry
  • Molecular Biology

Background:

  • Two-dimensional gel electrophoresis (2-DE) allows quantification of hundreds of protein abundances in biological samples.
  • Despite its reputation for being slow, 2-DE remains effective for specific proteomic analyses.

Purpose of the Study:

  • To review statistical tools for analyzing 2-DE data.
  • To provide guidelines for discovering and characterizing protein spots, including genetic variations, alternative splicing, and post-translational modifications (PTMs).

Main Methods:

  • Exploratory and confirmatory statistical analyses of protein spot data from 2-DE.
  • Case-specific guidelines for protein discovery and characterization.

Main Results:

  • 2-DE is still effective for identifying and quantifying proteins affected by genetic variations, alternative splicing, and PTMs.
  • Statistical tools can aid in the discovery of significant protein spots.

Conclusions:

  • 2-DE, combined with appropriate statistical methods, is a powerful tool for in-depth proteomic analysis.
  • This approach facilitates the characterization of protein families and their PTMs, offering insights into biological processes.