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Related Concept Videos

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...
Subcellular Fractionation01:32

Subcellular Fractionation

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.
Differential Centrifugation
Differential centrifugation is...
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...
Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
Export of Misfolded Proteins out of the ER01:32

Export of Misfolded Proteins out of the ER

After folding, the ER assesses the quality of secretory and membrane proteins. The correctly folded proteins are cleared by the calnexin cycle for transport to their final destination, while misfolded proteins are held back in the ER lumen. The ER chaperones attempt to unfold and refold the misfolded proteins but sometimes fail to achieve the correct native conformation. Such terminally misfolded proteins are then exported to the cytosol by ER-associated degradation or ERAD pathway for...

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Organelle proteomics experimental designs and analysis.

Laurent Gatto1, Juan Antonio Vizcaíno, Henning Hermjakob

  • 1Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK.

Proteomics
|November 17, 2010
PubMed
Summary

Accurate protein sub-cellular localization is crucial for understanding protein function. This review highlights the need for rigorous experimental design and data analysis in organelle proteomics to ensure high-quality, reproducible localization data.

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Area of Science:

  • Cellular Biology
  • Proteomics
  • Bioinformatics

Background:

  • Protein localization is fundamental to understanding biological function.
  • Advances in organelle proteomics necessitate improved experimental and analysis strategies.
  • Reliable sub-cellular localization assignment is critical for biological research.

Purpose of the Study:

  • To review current experimental designs and data analysis in organelle proteomics.
  • To emphasize the benefits of rigorous experimental and analysis design description.
  • To promote the generation of high-quality organelle localization data.

Main Methods:

  • Overview of qualitative and quantitative organelle proteomics experimental designs.
  • Discussion of associated data analysis methodologies.
  • Exploration of benefits of detailed experimental and analysis design dissemination.

Main Results:

  • Identified key benefits: design comparison, data validation, reproducibility, efficient data retrieval, and meta-analysis.
  • Highlighted the importance of formalizing experimental and analysis workflows.
  • Emphasized the impact on the quality of organelle localization data.

Conclusions:

  • Formalized experimental and analysis workflows are essential for organelle proteomics.
  • Improved design and description enhance data quality, reproducibility, and utility.
  • This approach benefits researchers and the broader scientific community.