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Related Concept Videos

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...
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 Proteasome Structure01:17

The Proteasome Structure

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...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...

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Related Experiment Video

Updated: Jun 4, 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

Ubiquitinated proteome: ready for global?

Yi Shi1, Ping Xu, Jun Qin

  • 1Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

Molecular & Cellular Proteomics : MCP
|February 23, 2011
PubMed
Summary

Identifying lysine ubiquitination sites is challenging. New affinity reagents and careful data analysis are crucial for accurate, large-scale detection of ubiquitination events in cells.

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Last Updated: Jun 4, 2026

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
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Profiling Ubiquitin and Ubiquitin-like Dependent Post-translational Modifications and Identification of Significant Alterations
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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:

  • Biochemistry
  • Molecular Biology
  • Proteomics

Background:

  • Ubiquitin (Ub) is a key post-translational modifier regulating cellular functions.
  • Large-scale profiling of lysine ubiquitination remains a significant challenge in proteomics.
  • Advancements in mass spectrometry and affinity purification have improved analysis of other modifications.

Purpose of the Study:

  • To review strategies for identifying ubiquitination sites.
  • To discuss challenges in analyzing ubiquitination data.
  • To highlight recent progress in large-scale ubiquitination detection.

Main Methods:

  • Utilizing novel Ub affinity reagents like Ub remnant antibodies and tandem Ub binding domains.
  • Employing mass spectrometry for proteome-wide analysis.
  • Reviewing various site identification strategies.

Main Results:

  • Recent development of Ub affinity reagents enables detection of hundreds of lysine ubiquitination events.
  • These tools facilitate relatively large-scale profiling of ubiquitination in human cells.
  • Challenges in data analysis require careful interpretation and orthogonal confirmation.

Conclusions:

  • New affinity reagents are advancing the field of lysine ubiquitination analysis.
  • Orthogonal confirmation and careful MS spectra interpretation are essential to minimize false positives.
  • Accurate identification of ubiquitination sites is critical for understanding cellular regulation.