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

Proteomics01:33

Proteomics

7.2K
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...
7.2K

You might also read

Related Articles

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

Sort by
Same author

Site Confidence Scores among All Available Structures to Help Infer Conformational Origins of Identified Cross-Links.

Journal of proteome research·2026
Same author

On the Feasibility of Clinical Studies with Cross-Linking Mass Spectrometry.

Journal of proteome research·2026
Same author

Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provide New Insight into Protein Conformational Plasticity within Organelles, Cells, and Tissues.

Journal of proteome research·2025
Same author

Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provides New Insight on Protein Conformational Plasticity within Organelles, Cells, and Tissues.

bioRxiv : the preprint server for biology·2024
Same author

Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research.

Scientific data·2024
Same author

Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines.

bioRxiv : the preprint server for biology·2024
Same journal

Identification of Age-Associated Circulating Proteins and Lipids in 3800 Comorbidity-Enriched Older Adults from Japan-Based Cohorts Using Olink Assays and MRM Mass Spectrometry.

Journal of proteome research·2026
Same journal

Molecular Solution to the Paradox of Ancient Brain Preservation.

Journal of proteome research·2026
Same journal

From Method-Defined Signals to Reference Measurement Procedures: Two Decades of Mass Spectrometry-Based ProGRP Quantification.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Extracellular Vesicle-Enriched Plasma Using Mag-Net for Biomarker Discovery in Pancreatic Ductal Adenocarcinoma.

Journal of proteome research·2026
Same journal

Computationally Efficient Bayesian Estimation of Graphical Networks for Omics Data.

Journal of proteome research·2026
Same journal

Hierarchy of MS-Based Evidence.

Journal of proteome research·2026
See all related articles

Related Experiment Video

Updated: Jun 9, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

11.9K

Combining Quantitative Proteomics and Interactomics for a Deeper Insight into Molecular Differences between Human

Anna A Bakhtina1, Helisa H Wippel1, Juan D Chavez1

  • 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.

Journal of Proteome Research
|October 25, 2024
PubMed
Summary
This summary is machine-generated.

This study used quantitative cross-linking and mass spectrometry to map protein interactome differences in HEK293, MCF-7, and HeLa cells. The findings reveal cell-specific interactome variations driven by proteome changes, offering insights into cellular functions.

Keywords:
cellular quantitative interactomehuman cell linemass spectrometryquantitative cross-linking

More Related Videos

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
12:53

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Published on: July 6, 2014

31.4K
Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
08:08

Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors

Published on: February 27, 2015

16.1K

Related Experiment Videos

Last Updated: Jun 9, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

11.9K
Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
12:53

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Published on: July 6, 2014

31.4K
Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
08:08

Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors

Published on: February 27, 2015

16.1K

Area of Science:

  • Biochemistry
  • Cell Biology
  • Proteomics

Background:

  • Cultivable cell lines are crucial in biomedical research, with functional profiles often determined by protein interactions (interactome).
  • Understanding cell line-specific interactomes is key to interpreting experimental results.

Purpose of the Study:

  • To quantitatively compare the large-scale protein interactome differences among three human cell lines: HEK293, MCF-7, and HeLa.
  • To investigate how proteome abundance and independently regulated interactome changes contribute to cell type-specific functional landscapes.

Main Methods:

  • Quantitative in vivo protein cross-linking coupled with mass spectrometry to analyze protein interactions.
  • Data-independent acquisition quantitative proteomics to measure proteome abundance levels.
  • Integration of interactome and proteome data for comprehensive analysis.

Main Results:

  • Highly reproducible quantitative interactome data (R² > 0.8) across biological replicates.
  • Identified cell type-specific interactome alterations linked to proteome adaptations and independent regulation.
  • Significant changes observed in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, and mitochondrial proteins.

Conclusions:

  • Quantitative cross-linking is a reproducible method for studying system-level interactome variations.
  • Combined quantitative interactomics and proteomics provide unique insights into cellular functional differences.
  • The study highlights the utility of these methods for understanding cell line-specific molecular mechanisms.