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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 15, 2025

Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

Published on: April 30, 2019

Cell shapes decode molecular phenotypes in image-based spatial proteomics.

Trang Le^1,2, William D Leineweber¹, Matheus P Viana³

¹Department of Bioengineering, Stanford University, Stanford, CA, USA.

Biorxiv : the Preprint Server for Biology

|June 4, 2025

Summary

This summary is machine-generated.

Cell shape significantly influences protein behavior and cellular fate, even within the same cell cycle phase. This study reveals how proteome organization relates to cell geometry, impacting cell function and response to drugs.

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Last Updated: Jun 15, 2025

Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

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Published on: April 30, 2019

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

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Published on: July 6, 2022

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization

Published on: October 29, 2019

Area of Science:

Cell Biology
Biophysics
Proteomics
Bioinformatics

Background:

Cellular and tissue diversity arises from basic cell shapes and biophysical constraints on cytoskeletal organization.
Cellular geometry is linked to biological processes like polarity, signaling, and morphogenesis.
The relationship between the entire proteome and cell shape is not well understood.

Purpose of the Study:

To perform an integrated analysis of organelle, pathway, and single protein levels in association with a 2D cellular shapespace.
To understand the orchestration of the whole proteome in relation to cell shape.
To analyze protein spatial localization shifts under drug perturbation using a shape-defined coordinate framework.

Main Methods:

Utilized over 1 million images of single cells from the Human Protein Atlas database.
Analyzed 11,998 proteins across 10 cell lines.
Integrated analysis of organelle, pathway, and single protein levels within a 2D cellular shapespace.

Main Results:

Cell and nuclear shapes form a shared continuum across cell lines.
Subcellular organelle topology varies by cell line but is robust within each cell line's shapespace.
Cells of different shapes in the same cell cycle phase may prepare for different fates; many non-cell cycle proteins show shape-based abundance variation.

Conclusions:

Cell shape is a critical determinant of proteome organization and cellular function.
Protein localization and abundance are significantly influenced by cell geometry.
A shape-based coordinate framework enables analysis of drug perturbation effects on protein localization.