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

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...

You might also read

Related Articles

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

Sort by
Same author

Cellular neighborhoods govern antitumor T-cell infiltration following anti-CTLA-4 in melanoma with primary resistance to anti-PD-1.

Cancer discovery·2026
Same author

Neoadjuvant PD-1 blockade in surgically resectable desmoplastic melanoma: cohort A of the phase 2 SWOG S1512 trial.

Nature cancer·2026
Same author

Detecting clinically relevant topological structures in multiplexed spatial proteomics using TopKAT.

Patterns (New York, N.Y.)·2026
Same author

Zalsupindole is a Nondissociative, Nonhallucinogenic Neuroplastogen with Therapeutic Effects Comparable to Ketamine and Psychedelics.

ACS chemical neuroscience·2025
Same author

Publisher Correction: Anti-PD-1 therapy in unresectable desmoplastic melanoma: the phase 2 SWOG S1512 trial.

Nature medicine·2025
Same author

Anti-PD-1 therapy in unresectable desmoplastic melanoma: the phase 2 SWOG S1512 trial.

Nature medicine·2025

Related Experiment Video

Updated: May 14, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Topological Data Analysis of Spatial Protein Expression in Multiplexed Spatial Proteomics Studies.

Sarah Samorodnitsky1,2, Michael C Wu1,2

  • 1Public Health Sciences Division, Fred Hutchinson Cancer Center.

Biorxiv : the Preprint Server for Biology
|May 13, 2026
PubMed
Summary

This study introduces TOASTER, a novel method for spatial proteomics analysis. TOASTER bypasses cell segmentation to directly link protein expression patterns to patient outcomes, improving accuracy and power.

More Related Videos

Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry
06:51

Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry

Published on: November 14, 2025

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging
08:40

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Published on: April 8, 2016

Related Experiment Videos

Last Updated: May 14, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry
06:51

Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry

Published on: November 14, 2025

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging
08:40

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Published on: April 8, 2016

Area of Science:

  • Biomedical Imaging
  • Computational Biology
  • Proteomics

Background:

  • Multiplexed spatial proteomics generates high-resolution tissue images, but pre-processing for cell segmentation and phenotyping can be error-prone.
  • Existing methods often overlook direct protein expression levels and rely on potentially inaccurate cell arrangements.
  • Emerging research indicates topological analysis of spatial proteomics data may offer greater analytical power.

Purpose of the Study:

  • To develop a novel method, TOASTER, for analyzing spatial proteomics data.
  • To circumvent the limitations of cell segmentation and phenotyping in spatial proteomics.
  • To associate continuous spatial protein expression directly with patient-level outcomes.

Main Methods:

  • TOASTER utilizes topological data analysis to characterize topological features in spatial protein expression.
  • It employs an adaptation of the Nelson-Aalen cumulative hazard function to summarize topological structure.
  • The method associates this summary with outcomes using functional data analysis, gridwise testing, or kernel association testing.

Main Results:

  • Simulations demonstrate TOASTER improves statistical power and controls Type I error rates.
  • The method shows robustness even with image artifacts like gaps or tears.
  • Application to triple-negative breast cancer data revealed associations between protein expression topology and immunotherapy response.

Conclusions:

  • TOASTER offers a powerful, segmentation-free approach for spatial proteomics.
  • It effectively links spatial protein expression patterns to patient outcomes.
  • This method enhances the analysis of complex biological systems and has implications for precision medicine.