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Related Concept Videos

Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Regulated Protein Degradation02:58

Regulated Protein Degradation

It is vital to regulate the activity of enzymatic as well as non-enzymatic proteins inside the cell. This can be achieved either through creating a balance between their rate of synthesis and degradation or regulating the intrinsic activity of the protein. Both these regulation mechanisms play an essential role in the normal functioning of cells.
Protein degradation plays two important roles in the cells. It helps to protect cells from misfolded or damaged proteins before they lead to a...
The Proteasome01:13

The Proteasome

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 (ubiquitin...
The Proteasome02:18

The Proteasome

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...
Proteomics01:33

Proteomics

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 proteomics...

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Related Experiment Video

Updated: May 20, 2026

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Quantitative proteomics to decipher ubiquitin signaling.

Ping-Chung Chen1, Chan Hyun Na, Junmin Peng

  • 1Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.

Amino Acids
|July 24, 2012
PubMed
Summary

Mass spectrometry-based proteomics advances the study of ubiquitin signaling, a key cellular process. This method identifies ubiquitin targets and modifications, aiding disease research.

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
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Comparative Strategies for Ubiquitination Detection in Mammalian Cell Lysates Using SMAD2/SMURF2 as a Model
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Comparative Strategies for Ubiquitination Detection in Mammalian Cell Lysates Using SMAD2/SMURF2 as a Model

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Area of Science:

  • Cellular biology
  • Biochemistry
  • Proteomics

Background:

  • Ubiquitin signaling is crucial for eukaryotic cellular processes.
  • Dysregulation of ubiquitin pathways is linked to numerous human diseases.
  • Mass spectrometry-based proteomics has become vital for studying ubiquitin.

Purpose of the Study:

  • To highlight the utility of mass spectrometry-based proteomics in ubiquitin research.
  • To demonstrate how quantitative proteomics reveals dynamic changes in the ubiquitinome.
  • To showcase the application of these methods in understanding disease pathogenesis.

Main Methods:

  • Utilizing mass spectrometry-based proteomics to identify the ubiquitinated proteome (ubiquitinome).
  • Employing quantitative strategies to detect dynamic changes in protein ubiquitination.
  • Profiling total cell lysate alongside the ubiquitinated proteome in parallel samples.

Main Results:

  • Identification of ubiquitinated proteins, modification sites, and ubiquitin chain linkages.
  • Detection of dynamic alterations in the ubiquitinome under various conditions.
  • Distinguishing functional ubiquitin targets from experimental noise through quantitative analysis.

Conclusions:

  • Quantitative proteomics is a powerful tool for dissecting ubiquitin signaling pathways.
  • This approach aids in identifying disease-relevant ubiquitin targets and understanding ubiquitin-like protein pathways.
  • Mass spectrometry-based proteomics significantly enhances the study of ubiquitin's role in health and disease.