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Proteomics

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...

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Related Experiment Video

Updated: Jun 29, 2025

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

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

Published on: July 6, 2022

A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data.

Sarah Samorodnitsky^1,2, Katie Campbell³, Antoni Ribas³

¹Public Health Sciences Division, Fred Hutch Cancer Center.

Biorxiv : the Preprint Server for Biology

|April 1, 2024

Summary

This summary is machine-generated.

A new method, SPatial Omnibus Test (SPOT), analyzes immune cell spatial clustering in tumors across multiple radii. This approach enhances the ability to link spatial organization to patient outcomes, offering valuable clinical insights.

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Last Updated: Jun 29, 2025

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

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

Published on: July 6, 2022

SpOT the Correct Tissue Every Time in Multi-tissue Blocks

SpOT the Correct Tissue Every Time in Multi-tissue Blocks

Published on: May 31, 2015

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

Area of Science:

Immunology
Computational Biology
Biostatistics

Background:

Spatial proteomics is crucial for understanding the tumor immune microenvironment.
Existing spatial clustering measures (e.g., Ripley's K) require a predefined radius, lacking consensus on optimal selection.
This limitation hinders robust analysis of spatial organization and patient outcomes.

Conclusions:

SPOT offers a comprehensive approach to assessing spatial immune cell organization in the tumor microenvironment.
The method provides a robust framework for identifying associations between spatial patterns and patient outcomes.
An R package and tutorial are available for broader application.