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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: Nov 30, 2025

Cell Type-specific Gene Expression Profiling in the Mouse Liver

Cell Type-specific Gene Expression Profiling in the Mouse Liver

Published on: September 17, 2019

Cell type-selective secretome profiling in vivo.

Wei Wei^1,2,3, Nicholas M Riley^3,4,5, Andrew C Yang⁶

¹Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

Nature Chemical Biology

|November 17, 2020

Summary

Researchers developed a new method to study secreted proteins from specific cells in mice. This proteomic atlas reveals cell-specific signaling molecules and nutrient-driven changes in liver cell secretions.

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Last Updated: Nov 30, 2025

Cell Type-specific Gene Expression Profiling in the Mouse Liver

Cell Type-specific Gene Expression Profiling in the Mouse Liver

Published on: September 17, 2019

"Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome

"Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome

Published on: March 24, 2023

Cell-Type Specific Protein Purification and Identification from Complex Tissues Using a Mutant Methionine tRNA Synthetase Mouse Line

Cell-Type Specific Protein Purification and Identification from Complex Tissues Using a Mutant Methionine tRNA Synthetase Mouse Line

Published on: April 13, 2022

Area of Science:

Proteomics
Cellular Biology
Biochemistry

Background:

Secreted polypeptides are crucial for intercellular and endocrine communication.
A comprehensive understanding of cellular secretomes in vivo has been limited.
Existing methods lack cell type-specificity for studying secreted proteins.

Purpose of the Study:

To develop a method for cell type-selective labeling and analysis of secreted proteins in vivo.
To create a proteomic atlas of key cell types' secretomes.
To investigate dynamic changes in secretomes, particularly in response to nutrients.

Main Methods:

Proximity biotinylation strategy for labeling secreted polypeptides.
Cell type-selective enrichment of biotinylated proteins from mouse blood plasma.
Proteomic analysis to identify and quantify secreted proteins.

Main Results:

Generated a proteomic atlas of hepatocyte, myocyte, pericyte, and myeloid cell secretomes.
Validated known cell type-specific secreted proteins and identified novel ones.
Discovered a nutrient-dependent reprogramming of the hepatocyte secretome, including unconventional secretion of BHMT.

Conclusions:

The developed strategy enables dynamic, cell type-specific dissection of the plasma proteome.
This approach provides insights into intercellular signaling mediated by secreted polypeptides.
Revealed previously undescribed nutrient-dependent regulation of cellular secretion.