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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 proteomics...

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Related Experiment Video

Updated: May 14, 2026

Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo

Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo

Published on: April 21, 2022

Exploring biological processes involved in embryonic stem cell differentiation by analyzing proteomic data.

Mohieddin Jafari¹, Mehdi Mirzaie, Mehdi Sadeghi

¹Shahid Beheshti University of Medical Sciences, Tehran, Iran. mjafari@ipm.ir

Biochimica Et Biophysica Acta

|February 19, 2013

Summary

Proteomics reveals distinct active processes during embryonic stem cell differentiation. Analyzing protein concentration profiles identified new stages in this crucial developmental process.

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Area of Science:

Cellular biology
Developmental biology
Proteomics

Background:

Proteins execute diverse cellular functions at varying concentrations, making proteomics a powerful tool for understanding biological processes.
Gene ontology offers a framework for protein annotation, but condition-specific functional details often require dynamic concentration data.
Changes in protein concentration are assumed to directly correlate with biological activity, enabling functional inference from proteomic profiles.

Purpose of the Study:

To analyze time-course proteomic data from embryonic stem cell (ESC) differentiation into embryoid bodies (EBs).
To identify distinct active biological processes and their temporal dynamics during early differentiation using protein concentration profiles.
To propose novel change points or stages in embryonic differentiation based on proteomic data analysis.

Main Methods:

Utilized time-course proteomic datasets spanning twenty days of ESC to EB differentiation.
Employed hierarchical clustering to group proteins with similar temporal concentration patterns.
Analyzed clustered protein profiles to identify distinct active processes and their dynamic changes.

Main Results:

Identified eleven distinct active biological processes characterized by unique protein concentration profiles during early differentiation.
Demonstrated that protein concentration dynamics can effectively delineate stages of embryonic development.
Revealed specific temporal patterns indicative of key events in the differentiation trajectory.

Conclusions:

Proteomic profiling provides a detailed view of cellular events, surpassing traditional mRNA studies for dynamic process elucidation.
The identified eleven active processes and their distinct profiles offer insights into the mechanisms of ESC differentiation.
The study suggests new, data-driven change points for understanding the stages of embryonic differentiation.