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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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The Proteasome Structure01:17

The Proteasome Structure

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The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
The proteasome is an...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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The Proteasome01:13

The Proteasome

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Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
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The Proteasome02:18

The Proteasome

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Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
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Related Experiment Video

Updated: Mar 10, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Proteomes, Their Compositions and Their Sources.

Anna Kwasnik1, Claire Tonry1, Angela Mc Ardle1

  • 1School of Medicine and Medical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.

Advances in Experimental Medicine and Biology
|December 16, 2016
PubMed
Summary
This summary is machine-generated.

Biological samples are crucial for mass spectrometry-based proteomics research. Analyzing tissues and body fluids aids in discovering disease markers, developing new drugs, and understanding drug mechanisms and side effects.

Keywords:
Biological fluidsCell cultureSample origin

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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
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Area of Science:

  • Proteomics
  • Biomedical Research
  • Biotechnology

Background:

  • Biological samples from human and animal origins are essential in diverse scientific fields.
  • These samples include organs, tissues, cells, and body fluids like blood and saliva.
  • Sample types and physiological states dictate their application in research and diagnostics.

Purpose of the Study:

  • To highlight the utility of biological samples in mass spectrometry-based proteomics.
  • To explain the role of different sample types in disease mechanism and drug discovery.
  • To underscore the importance of sample analysis for developing diagnostic strategies and therapeutics.

Main Methods:

  • Utilizing various biological sample types (organs, tissues, cells, body fluids).
  • Employing mass spectrometry-based proteomics for sample analysis.
  • Applying techniques like Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for cell-based studies.

Main Results:

  • Proteomics analysis of body fluids and tissues identifies protein markers for distinguishing physiological and pathophysiological states.
  • Cell line studies, particularly with SILAC, elucidate disease mechanisms and drug functions.
  • Data generated aids in developing novel diagnostic strategies and pharmaceutical treatments.

Conclusions:

  • Biological samples are indispensable for advancing proteomics research.
  • Proteomics analysis of diverse samples drives innovation in disease diagnostics and drug development.
  • Understanding sample-specific applications is key to effective research and therapeutic discovery.