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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: Jul 17, 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 Kitata, Marija Velickovic, Zhangyang Xu

Biorxiv : the Preprint Server for Biology

|August 30, 2023

Summary

This summary is machine-generated.

A new method called wcSOP enables robust single voxel proteomics, providing spatial resolution of protein signatures within tissues. This technique allows for detailed proteome mapping of tissue microenvironments, advancing spatial proteomics research.

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Last Updated: Jul 17, 2025

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

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Published on: November 15, 2017

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Published on: October 20, 2020

Area of Science:

Proteomics
Biotechnology
Spatial Biology

Background:

Bulk tissue proteomics lacks spatial resolution, hindering the analysis of tissue microenvironments and heterogeneity.
Current methods cannot map proteomes at the single voxel level, limiting understanding of cellular and tissue organization.
Advanced mass spectrometry (MS) offers genome-scale proteome coverage but requires spatial context for comprehensive analysis.

Approach:

Introduced the integrated wet collection of single tissue voxel and Surfactant-assisted One-Pot (wcSOP) voxel processing method.
Utilized buffer droplet-assisted wet collection of laser-captured microdissected (LCM) single tissue voxels into PCR tube caps.
Employed MS-compatible surfactant-assisted one-pot voxel processing within the collection cap for label-free quantification.

Key Points:

Achieved reproducible label-free quantification of ~900 proteins from 20 μm voxels (near single-cell resolution) and ~4,600 proteins from 200 μm voxels (~100 cells) in human spleen tissue.
Identified 100s-1000s of spatially resolved protein signatures with differential expression between spleen red and white pulp regions.
Enriched region-specific signaling pathways from single voxel proteomics data and validated MS quantitation using CODEX imaging.

Conclusions:

The wcSOP-MS method enables robust, label-free single voxel proteomics with high throughput.
This technique provides unprecedented spatial resolution for proteome mapping within complex tissues.
wcSOP-MS paves the way for routine spatial proteomics and detailed analysis of tissue microenvironments.