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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
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...

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...

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Related Experiment Video

Updated: Feb 18, 2026

Oligopeptide Competition Assay for Phosphorylation Site Determination

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

Accurate phosphorylation site localization using phospho-brackets.

Kaijie Xiao¹, Yun Shen¹, Shasha Li¹

¹School of Chemical Science & Engineering, Tongji University, Shanghai 200092, China; Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.

Analytica Chimica Acta

|November 16, 2017

Summary

This summary is machine-generated.

We developed P-bracket, a novel method using complementary product ions, for accurate protein phosphorylation site localization. This technique enhances phosphopeptide identification confidence without needing further control experiments.

Keywords:

False localization rate(FLR)P-bracket Phosphorylation Site localization Site-determining ions

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Last Updated: Feb 18, 2026

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Published on: May 18, 2017

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Published on: May 3, 2018

Area of Science:

Biochemistry
Proteomics
Analytical Chemistry

Background:

Protein phosphorylation is a critical post-translational modification regulating numerous cellular processes.
Tandem mass spectrometry, particularly with higher-energy collisional dissociation (HCD), is a powerful tool for identifying phosphopeptides.
Accurate localization of phosphorylation sites remains a significant challenge in proteomics.

Purpose of the Study:

To develop a novel method, P-bracket, for accurate and confident phosphosite localization.
To utilize direct experimental evidence of site-determining product ions for improved localization.
To eliminate the need for additional False Localization Rate (FLR) control experiments.

Main Methods:

Development of the P-bracket concept, defined as a complementary product ion pair.
Experimental validation using synthetic phosphopeptides and phosphopeptide reference libraries.
Benchmarking against two HeLa phosphopeptide LC-MS/MS (HCD) datasets.

Main Results:

P-bracket successfully localized phosphorylation sites using direct experimental evidence.
The method was validated across various synthetic and real-world phosphopeptide datasets.
Demonstrated accurate phosphosite localization without reliance on FLR control.

Conclusions:

P-bracket provides a robust approach for accurate phosphosite localization.
This method significantly enhances the confidence of phosphopeptide identification.
P-bracket facilitates downstream structural and functional studies of phosphoproteins.