Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Subcellular Fractionation01:32

Subcellular Fractionation

9.4K
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...
9.4K
Proteomics01:33

Proteomics

10.1K
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...
10.1K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A Unique Intraexonic Splicing Mechanism in the Immunoglobulin Domain of NKp30 Produces a Surface-Expressed Receptor With Altered Ligand Specificity.

European journal of immunology·2026
Same author

Biological and clinical characteristics of <i>ETV6</i>::<i>RUNX1</i>-like ALL.

HemaSphere·2026
Same author

TCR T cells targeting IgA- and IgG-expressing multiple myeloma.

Blood·2026
Same author

CaRinDB: an integrated database of common cancer mutations and residue interaction network parameters.

Bioinformatics advances·2026
Same author

CD Molecules Nomenclature 2025: Antibody Validation and Expression Profiling of Immune System G Protein-Coupled Receptors.

European journal of immunology·2025
Same author

An Elastin-like Polymer Targeting Vascular Endothelial Growth Factor Receptor-1 Reduces Survival in Serum-Starved Endothelial Cells.

Biochemical engineering journal·2025

Related Experiment Video

Updated: Mar 15, 2026

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach
04:25

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach

Published on: August 8, 2025

1.4K

MetaMass, a tool for meta-analysis of subcellular proteomics data.

Fridtjof Lund-Johansen1,2, Daniel de la Rosa Carrillo1,3, Adi Mehta1,4

  • 1Department of Immunology, Oslo University Hospital, Oslo, Norway.

Nature Methods
|August 30, 2016
PubMed
Summary

MetaMass is a new tool for analyzing subcellular proteomics data. It uses standardized markers to map protein locations, revealing issues with fractionation protocols and database biases, improving data transparency.

More Related Videos

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

3.7K
A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry
08:04

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

Published on: March 13, 2014

12.7K

Related Experiment Videos

Last Updated: Mar 15, 2026

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach
04:25

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach

Published on: August 8, 2025

1.4K
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

3.7K
A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry
08:04

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

Published on: March 13, 2014

12.7K

Area of Science:

  • Proteomics
  • Cell Biology
  • Bioinformatics

Background:

  • Subcellular proteomics is crucial for understanding cell function.
  • Accurate mapping of protein localization is essential but challenging.
  • Existing methods lack standardization and can introduce biases.

Purpose of the Study:

  • To introduce MetaMass, a novel tool for analyzing subcellular proteomics data.
  • To enhance the transparency and reproducibility of subcellular localization studies.
  • To identify and address variations in subcellular fractionation and annotation.

Main Methods:

  • Developed MetaMass, a tool utilizing standardized lists of subcellular markers.
  • Applied MetaMass to analyze data from 11 independent subcellular proteomics studies.
  • Mapped the subcellular locations of 5,970 proteins using the MetaMass tool.

Main Results:

  • Identified significant variations in the performance of subcellular fractionation protocols across studies.
  • Uncovered systematic biases present in commonly used protein annotation databases.
  • Successfully mapped the locations of thousands of proteins, highlighting data inconsistencies.

Conclusions:

  • MetaMass provides a standardized approach to subcellular proteomics data analysis.
  • The tool reveals critical limitations in current experimental protocols and annotation resources.
  • MetaMass is expected to improve the reliability and reproducibility of subcellular proteomics research.