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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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Related Experiment Video

Updated: Aug 10, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Proteome Coverage after Simultaneous Proteo-Metabolome Liquid-Liquid Extraction.

Alienke van Pijkeren1,2, Anna-Sophia Egger1, Madlen Hotze1

  • 1Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, A-6020, Austria.

Journal of Proteome Research
|February 10, 2023
PubMed
Summary

Urea is the most efficient agent for extracting proteins from samples prepared using simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE). This method is crucial for systems biology, enabling analysis of both proteomes and metabolomes from a single sample.

Keywords:
SP3bottom-up proteomicsin-solution digestlabel free quantificationmass spectrometrymetabolomicsproteomicssample preparationsimultaneous proteo-metabolomics

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A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample
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Area of Science:

  • Systems biology
  • Biochemistry
  • Analytical chemistry

Background:

  • Simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) is vital for systems biology, isolating both the metabolome and proteome from a single sample.
  • The proteome, isolated as a pellet in SPM-LLE, requires efficient solubilization for quantitative proteomic analysis.
  • Extraction efficiency and proteome coverage are critical for maximizing information gained from proteomic studies.

Purpose of the Study:

  • To evaluate the performance of sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS), and urea for proteome extraction from SPM-LLE interphase pellets.
  • To compare the effectiveness of these agents when extracting from interphase pellets versus direct cell lysis.
  • To identify the optimal extraction agent for simultaneous proteo-metabolome analysis.

Main Methods:

  • Investigated proteome coverage and extraction efficiency using two surfactants (SDC, SDS) and urea on interphase pellets from methanol-chloroform based SPM-LLE.
  • Compared extraction performance from interphase pellets versus direct cell lysis.
  • Quantified lipids and polar metabolites in chloroform and methanol extracts to assess metabolome recovery.

Main Results:

  • Proteome coverage was similar across SDC, SDS, and urea for SPM-LLE interphase pellets, but extraction efficiencies varied significantly.
  • SDS enriched basic proteins (ribosomal, ribonuclear), while urea demonstrated superior extraction efficiency for simultaneous proteo-metabolome analysis.
  • Surfactants performed better with direct cell lysis, whereas urea excelled with interphase pellets, particularly for proteins in metabolic pathways.

Conclusions:

  • Urea is the superior agent for proteome extraction from SPM-LLE interphase pellets compared to SDC and SDS.
  • Urea's effectiveness in extracting proteins associated with metabolic pathways makes it ideal for simultaneous proteo-metabolome analysis.
  • The choice of extraction method (interphase pellet vs. direct lysis) significantly impacts the performance of different agents for quantitative proteomics.