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

SpatioTemporal Omics Consortium: a global effort for biological discovery across species, space and time.

Nature methods·2026
Same author

Transcriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance.

Science advances·2026
Same author

Comparative genomic analysis of clinically relevant human skin-associated fungi.

Nature communications·2026
Same author

Proteomics reveals spatial and molecular heterogeneities in advanced atherosclerotic carotid artery plaques.

Nature cardiovascular research·2026
Same author

NLRP1 inflammasome activation in skin equivalents reveals mechanistic insights into the roles of keratinocytes in psoriasis.

Cell death & disease·2026
Same author

NGFR induces melanoma invasion and immunotherapy resistance through myosin light chain 2 modulation.

The EMBO journal·2026

Related Experiment Video

Updated: Jul 18, 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

12.0K

Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel.

Marvin Thielert1, Ericka Cm Itang1, Constantin Ammar1

  • 1Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.

Molecular Systems Biology
|August 21, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces multiplexed data-independent acquisition (mDIA) for enhanced single-cell proteomics, enabling deeper protein quantification and higher throughput for precision oncology applications.

Keywords:
DIAdimethyl labelingmultiplexingsingle cellsspatial proteomics

More Related Videos

Counting Proteins in Single Cells with Addressable Droplet Microarrays
12:25

Counting Proteins in Single Cells with Addressable Droplet Microarrays

Published on: July 6, 2018

8.6K
Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples
08:18

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Published on: April 7, 2023

1.6K

Related Experiment Videos

Last Updated: Jul 18, 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

12.0K
Counting Proteins in Single Cells with Addressable Droplet Microarrays
12:25

Counting Proteins in Single Cells with Addressable Droplet Microarrays

Published on: July 6, 2018

8.6K
Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples
08:18

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Published on: April 7, 2023

1.6K

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Single-cell analysis

Background:

  • Single-cell proteomics is crucial for understanding biological heterogeneity but faces limitations in depth, throughput, and robustness.
  • Existing methods struggle to provide comprehensive protein-level insights from individual cells.

Purpose of the Study:

  • To develop a streamlined, multiplexed workflow for enhanced single-cell proteomics.
  • To improve proteomic depth, throughput, and robustness in single-cell protein analysis.
  • To apply the new workflow to identify proteomic signatures in tumor microenvironments for precision oncology.

Main Methods:

  • Development of a streamlined multiplexed data-independent acquisition (mDIA) workflow.
  • Automated dimethyl labeling for bulk or single-cell samples.
  • Lys-N digestion enabling five-plex quantification at MS1 and MS2 levels.
  • Utilization of a reference channel with the RefQuant algorithm for enhanced quantification.
  • Integration of mDIA with spatial proteomics for increased throughput.

Main Results:

  • The mDIA workflow achieves automated, complete dimethyl labeling without loss of proteomic depth.
  • Five-plex quantification is enabled at both MS1 and MS2 levels.
  • The RefQuant algorithm confidently quantifies twice as many proteins per single cell compared to previous methods.
  • The workflow supports routine analysis of 80 single cells per day.
  • Combined mDIA and spatial proteomics increased Deep Visual Proteomics throughput seven-fold for microdissection and four-fold for MS analysis.

Conclusions:

  • The developed mDIA workflow significantly enhances proteomic depth and throughput for single-cell analysis.
  • This advancement enables confident quantification of more proteins per cell, improving biological insights.
  • Application to melanoma revealed proteomic signatures within tumor microenvironments, highlighting potential for precision oncology.