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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 homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
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Cytokinesis segregates a cell’s chromosomes and organelles into its daughter cells. Organelles divide and grow prior to cell division but cannot be synthesized de novo; therefore, cells must receive at least one copy of each organelle to survive. Currently, many of the details of how the organelles are distributed are not yet fully elucidated.
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One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry out specialized functions. Since biological membranes are only selectively permeable to solutes, they help create a compartment with controlled conditions inside an organelle. These microenvironments are tailored to the organelle's specific functions and help isolate them from the surrounding cytosol.
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Related Experiment Video

Updated: Jan 9, 2026

The CryoAPEX Method for Electron Microscopy Analysis of Membrane Protein Localization Within Ultrastructurally-Preserved Cells
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APEX2 and TurboID define unique subcellular proteomes.

Alexandria S Battison1, Jeremy L Balsbaugh2, Jeremy C Borniger3

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.

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|December 10, 2025
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Summary
This summary is machine-generated.

Choosing the right proximity labeling enzyme is crucial for accurate proteome mapping. TurboID and APEX2 offer distinct advantages for different cellular proteomic studies.

Keywords:
APEXCellular compartmentsProteomicsProximity labelingTurboID

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Area of Science:

  • Proteomics
  • Cell Biology
  • Biochemistry

Background:

  • Proximity labeling is a key technique for mapping local proteomes.
  • Peroxidase-based (APEX) and biotin-ligase-based (BioID) reagents are common.
  • Enzyme choice can introduce proteomic biases.

Purpose of the Study:

  • To compare proximity labeling enzymes TurboID and APEX2.
  • To analyze compartment-specific proteome enrichment in HEK293 cells.
  • To evaluate enzyme-specific biases and protease digestion effects.

Main Methods:

  • Proximity labeling using TurboID and APEX2 in HEK293 cells.
  • Compartment isolation (cytosol, nucleus, membrane).
  • Mass spectrometry-based proteomic analysis with trypsin and GluC digestion.

Main Results:

  • Both TurboID and APEX2 enriched compartment-specific proteomes.
  • TurboID identified more membrane proteins and RNA-processing proteins.
  • APEX2 enriched metabolic pathway proteins; protease choice impacts bias.

Conclusions:

  • TurboID is suitable for broad proteomic studies, APEX2 for specific pathways.
  • Enzyme and protease selection critically impacts proximity labeling outcomes.
  • Strategic choices enhance cellular proteome mapping accuracy.