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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 2, 2025

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

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

Published on: November 15, 2017

Robust collection and processing for label-free single voxel proteomics.

Reta Birhanu Kitata¹, Marija Velickovic², Zhangyang Xu¹

¹Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.

Nature Communications

|January 13, 2025

Summary

This summary is machine-generated.

A new method called Surfactant-assisted One-Pot voxel processing (wcSOP) enables robust single voxel proteomics. This technique allows for detailed spatial proteome mapping of tissue microenvironments, revealing region-specific protein signatures.

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Last Updated: Jun 2, 2025

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

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

Published on: November 15, 2017

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

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Published on: April 19, 2019

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:

Proteomics
Biotechnology
Tissue Microenvironment Analysis

Background:

Bulk tissue proteomics lacks spatial resolution, obscuring cellular heterogeneity.
Mapping tissue microenvironments requires methods with high spatial resolution.

Purpose of the Study:

To develop a robust method for label-free single voxel proteomics.
To enable spatial proteome mapping of tissue microenvironments.

Main Methods:

Integrated wet collection of single microscale tissue voxels.
Surfactant-assisted One-Pot voxel processing (wcSOP) method.
Laser capture microdissection (LCM) for voxel isolation.

Main Results:

Reproducible quantification of ~900 proteins from 20µm voxels (~1 cell region).
Quantification of ~4600 proteins from 200µm voxels (~100 cell region).
Demonstrated applicability to fresh frozen, OCT-embedded, and FFPE human tissues.

Conclusions:

wcSOP enables robust, label-free single voxel proteomics.
The method reveals spatially resolved protein signatures and signaling pathways.
wcSOP-MS facilitates routine spatial proteomics and tissue microenvironment analysis.