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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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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Related Experiment Video

Updated: Jul 1, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools.

Ara Lee1,2, Gihyun Sung1,2, Sanghee Shin3,4

  • 1Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea.

Nature Communications
|February 29, 2024
PubMed
Summary

OrthoID is a new proteomics method that identifies proteins at organelle contact sites. This technique uses engineered enzymes to label and enrich proteins, revealing their dynamic roles in cellular processes like mitophagy.

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Area of Science:

  • Cell Biology
  • Proteomics
  • Biochemistry

Background:

  • Identifying proteins at organelle contact sites, like mitochondria-associated endoplasmic reticulum membranes (MAM), is crucial for understanding cellular functions.
  • The dynamic nature of these proteins presents significant challenges for traditional proteomic methods.

Purpose of the Study:

  • To develop a novel proteomic method, OrthoID, for identifying and analyzing proteins at organelle contact sites.
  • To investigate the spatiotemporal dynamics of proteins at the ER-mitochondria interface during cellular processes such as mitophagy.

Main Methods:

  • OrthoID employs engineered enzymes TurboID and APEX2 for orthogonal biotinylation (Bt) and adamantylation (Ad) of proximal proteins.
  • High-affinity binding pairs, streptavidin-biotin (SA-Bt) and cucurbit[7]uril-adamantane (CB[7]-Ad), enable selective enrichment of labeled proteins.
  • The method was applied to study proteins at the mitochondria-ER contact site.

Main Results:

  • OrthoID successfully identified protein candidates at the ER-mitochondria contact site, including the previously uncharacterized protein LRC59.
  • The study tracked dynamic changes in protein sets at MAM during mitophagy.
  • Demonstrated the capability to analyze spatiotemporal protein localization and structural alterations.

Conclusions:

  • OrthoID is a powerful tool for identifying and analyzing proteins at organelle contact sites.
  • The method facilitates the study of dynamic protein behaviors in vital cellular processes.
  • OrthoID provides new insights into the molecular mechanisms underlying mitophagy and other cellular events.