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Related Concept Videos

Proteomics01:33

Proteomics

9.2K
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...
9.2K

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Related Experiment Video

Updated: Dec 29, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Proteomic Protocols for Differential Protein Expression Analyses.

Bent Honoré1

  • 1Department of Biomedicine, Aarhus University, Aarhus C, Denmark. bh@biomed.au.dk.

Methods in Molecular Biology (Clifton, N.J.)
|February 1, 2020
PubMed
Summary
This summary is machine-generated.

This study details sample preparation protocols for differential protein expression analysis using nano liquid chromatography-tandem mass spectrometry (nLCMS/MS). Methods cover diverse sample types and support label-free quantification or tandem mass tag labeling for proteomics research.

Keywords:
CellsDifferential protein expression analysisFFPELabel-free quantificationPlasmaProteomicsPull-downsSerumSpin filter device-based preparationTMT labelingTissuenLC-MS/MS

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Area of Science:

  • Proteomics
  • Biochemistry
  • Analytical Chemistry

Background:

  • Differential protein expression analysis is crucial for understanding biological processes and disease mechanisms.
  • Standardized and versatile sample preparation methods are essential for reliable proteomics studies.
  • Nano liquid chromatography-tandem mass spectrometry (nLCMS/MS) is a powerful technique for protein quantification.

Purpose of the Study:

  • To describe robust protocols for preparing diverse biological samples for nLCMS/MS-based proteomics.
  • To provide a unified sample preparation strategy applicable to various biological matrices.
  • To enable both label-free quantification and tandem mass tag (TMT) labeling approaches.

Main Methods:

  • Sample preparation utilizes spin filter devices with sodium deoxycholate (SDC) for efficient protein extraction.
  • Detergent removal is achieved via ethyl acetate phase extraction, compatible with downstream mass spectrometry.
  • Protocols accommodate fresh frozen tissue, FFPE tissue, cells, pull-downs, immunoprecipitations, and biofluids (plasma/serum).

Main Results:

  • The described method effectively processes a wide range of sample types for nLCMS/MS analysis.
  • The protocol is adaptable for both label-free quantification (LFQ) and TMT-labeled proteomics.
  • Considerations for comparative proteomics in transplantation and xenotransplantation studies are highlighted.

Conclusions:

  • A versatile and efficient sample preparation protocol is presented for differential protein expression studies using nLCMS/MS.
  • The method supports various sample types and labeling strategies, enhancing its applicability in proteomics research.
  • Careful consideration of sample comparability is advised for accurate interpretation of proteomic data, especially in comparative studies.