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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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Updated: Mar 3, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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In-Depth Proteome Coverage by Improving Efficiency for Membrane Proteome Analysis.

Qun Zhao1, Fei Fang1,2, Yichu Shan1

  • 1Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian 116023, China.

Analytical Chemistry
|April 25, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces a new sequential extraction method using urea and C12Im-Cl to improve proteome coverage, especially for hydrophobic proteins. This novel approach significantly increases identified proteins and reduces analysis time for comprehensive proteomic analysis.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Analytical Chemistry

Background:

  • Human proteome mapping is advancing, but sample preparation efficiency, particularly for membrane proteins, requires enhancement.
  • Current methods often struggle with comprehensive recovery of hydrophobic proteins and are affected by high-abundance soluble proteins.

Purpose of the Study:

  • To develop a novel sequential extraction strategy to improve proteome coverage.
  • To enhance the recovery of hydrophobic proteins and mitigate the suppression effect of abundant soluble proteins.
  • To establish a new benchmark for HeLa cell proteome dataset size and analysis efficiency.

Main Methods:

  • Sequential extraction of proteins using 8 M urea followed by 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl).
  • In situ sample preparation and separation utilizing diverse stationary phases.
  • High-throughput mass spectrometry for protein identification and quantification.

Main Results:

  • Identification of over 9810 gene products, representing the largest HeLa cell proteome dataset to date.
  • Achieved coverage across 8 orders of magnitude of protein abundance.
  • Demonstrated increased protein identification numbers and reduced analysis time compared to previous studies.

Conclusions:

  • The sequential urea and C12Im-Cl extraction strategy significantly enhances proteome coverage.
  • This method is effective for recovering hydrophobic proteins and reducing interference from abundant soluble proteins.
  • The developed approach offers a powerful tool for achieving unprecedented proteome coverage in biological samples.