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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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Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...

Protein Kinases and Phosphatases

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
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Phosphorylation

Phosphorylation

The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...

Phosphorylation

Phosphorylation

The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...

Phosphoinositides and PIPs

Phosphoinositides and PIPs

Phosphoinositides are a group of phospholipids containing a glycerol backbone with two fatty acid chains and a phosphate attached to a myoinositol sugar ring. The inositol head group extends into the cytoplasm, where it is modified by adding phosphate groups to form phosphatidylinositol phosphates or PIPs.
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Related Experiment Video

Updated: Jul 5, 2026

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

Published on: October 12, 2009

Phosphoproteomics.

Jun Zhong¹, Henrik Molina, Akhilesh Pandey

¹Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

Current Protocols in Protein Science

|April 23, 2008

Summary

This summary is machine-generated.

This study details methods for enriching phosphorylated proteins and peptides to analyze the phosphoproteome. Techniques include antibody enrichment and titanium dioxide chromatography for studying cellular signaling dynamics.

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Area of Science:

Cellular Biology
Biochemistry
Proteomics

Background:

Protein phosphorylation is a key regulatory mechanism controlling cellular processes like proliferation, migration, and metabolism.
The phosphoproteome encompasses all phosphorylated proteins, their modification sites, and dynamic changes in response to stimuli.

Purpose of the Study:

To provide robust methods for enriching phosphorylated proteins and peptides.
To enable detailed analysis of the phosphoproteome and its dynamics.

Main Methods:

Enrichment of phosphoproteins using anti-phosphotyrosine antibodies.
Enrichment of phosphopeptides via titanium dioxide chromatography.
Detergent-free cell lysis and protein fractionation protocols.
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for dynamic studies.

Main Results:

Established protocols for effective enrichment of phosphorylated proteins and peptides.
Demonstrated utility of SILAC for tracking dynamic changes in phosphorylation.
Provided a comprehensive approach to phosphoproteome analysis.

Conclusions:

The presented methods facilitate detailed investigation of the phosphoproteome.
These techniques are crucial for understanding cellular signaling pathways and responses to stimuli.
The study offers a valuable resource for researchers in cell signaling and proteomics.