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

You might also read

Related Articles

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

Sort by
Same author

Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2.

Nature communications·2026
Same author

Leveraging nanoparticle protein corona to advance plasma proteome profiling.

Nature communications·2026
Same author

Integrated top-down and bottom-up proteomics enables precise characterization of proteoforms within the protein corona.

Nature communications·2026
Same author

Spatiotemporal control of PIWI compartmentalization by mitochondrial scaffolds defines pachytene piRNA pathway organization.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Recent Advances (2023-2025) of Capillary Electrophoresis-Mass Spectrometry (CE-MS) for Top-Down Proteomics.

Mass spectrometry reviews·2026
Same author

Top-Down Proteomics of Zebrafish Brain Regions Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry.

Journal of proteome research·2026

Related Experiment Video

Updated: Dec 21, 2025

Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry
11:12

Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry

Published on: February 7, 2022

12.0K

Toward a Universal Sample Preparation Method for Denaturing Top-Down Proteomics of Complex Proteomes.

Zhichang Yang1, Xiaojing Shen1, Daoyang Chen1

  • 1Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824 United States.

Journal of Proteome Research
|May 19, 2020
PubMed
Summary

A new universal sample preparation method using membrane ultrafiltration (MU) enhances denaturing top-down proteomics (dTDP). This approach improves proteoform identification accuracy and protein recovery in complex biological samples.

Keywords:
CZE-MS/MSPTMsSDSSP3chloroform−methanol precipitationdenaturing top-down proteomicshistonemembrane proteinsmembrane ultrafiltrationsample preparation

More Related Videos

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
10:05

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

9.9K
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

12.5K

Related Experiment Videos

Last Updated: Dec 21, 2025

Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry
11:12

Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry

Published on: February 7, 2022

12.0K
Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
10:05

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Published on: October 24, 2018

9.9K
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

12.5K

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Standardized sample preparation is crucial for advancing denaturing top-down proteomics (dTDP).
  • Current methods require optimization for high protein recovery, minimal bias, reproducibility, and mass spectrometry (MS) compatibility.

Purpose of the Study:

  • To develop and evaluate a universal and standardized sample preparation method for dTDP.
  • To compare membrane ultrafiltration (MU), chloroform-methanol precipitation (CMP), and single-spot solid-phase (SP3) methods for proteoform cleanup.

Main Methods:

  • Proteins were extracted using a lysis buffer containing sodium dodecyl sulfate (SDS).
  • Proteoform cleanup was performed using MU, CMP, and SP3 methods.
  • Samples were analyzed using single-shot capillary zone electrophoresis-MS/MS (CZE-MS/MS).

Main Results:

  • The MU method demonstrated superior performance, yielding high and reproducible protein recovery from *Escherichia coli* (59 ± 3%) and human HepG2 cells (86 ± 5%) with minimal bias.
  • CZE-MS/MS analysis of MU-prepared samples identified 821 proteoforms in *E. coli* and 516 in HepG2 cells.
  • 94 histone proteoforms with various post-translational modifications were identified in HepG2 cells, and a significant proportion of identified proteins were membrane proteins.

Conclusions:

  • The combination of SDS-based protein extraction and MU-based cleanup offers a promising universal sample preparation strategy for dTDP.
  • This method enhances the scale and accuracy of proteoform delineation in complex biological systems.