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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: Apr 23, 2026

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 Le¹, William D Leineweber², Matheus P Viana³

¹Department of Bioengineering, Stanford University, Stanford, CA, USA; Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.

|April 21, 2026

Summary

This summary is machine-generated.

Cellular shapes are linked to protein organization and cell fate. This study reveals how cell and nuclear shapes form a continuum, influencing protein localization and cellular responses to drugs.

Keywords:

cell shape interpretable machine learning molecular variation morphological variation single cell spatial proteomics

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Last Updated: Apr 23, 2026

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

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Published on: April 30, 2019

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Published on: November 14, 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

Area of Science:

Cell Biology
Biophysics
Proteomics

Background:

Cellular and tissue structures originate from diverse cell shapes governed by biophysical constraints.
The relationship between signaling pathways and cellular geometry is known, but whole-proteome orchestration concerning cell shape remains under-investigated.

Purpose of the Study:

To explore whole-proteome orchestration in association with cell shape.
To analyze organelle, pathway, and single-protein levels in relation to cellular shapespace.
To investigate protein spatial localization shifts under drug perturbation using a shape-based framework.

Main Methods:

Analysis of over 1 million single cells from 11 cell lines using the Human Protein Atlas.
Single-cell proteomics and imaging to assess protein levels and localization.
Development of a shape-based coordinate framework for spatial analysis.

Main Results:

Cell and nuclear shapes across different cell lines form a shared continuum.
Subcellular organelle topology is cell-line specific but consistent within each cell line's shapespace.
Non-cell-cycle proteins show shape-based abundance variations, suggesting shape influences cell fate preparation.

Conclusions:

Cell shape is a fundamental organizing principle in cellular architecture and function.
Protein localization and abundance are significantly influenced by cellular geometry.
A shape-based framework can reveal dynamic protein distribution changes, offering insights into drug responses.