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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

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...

Protein Kinases and Phosphatases

Protein Kinases and Phosphatases

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

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Related Experiment Video

Updated: Mar 21, 2026

Oligopeptide Competition Assay for Phosphorylation Site Determination

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

Doubling down on phosphorylation as a variable peptide modification.

¹Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA. bret.cooper@ars.usda.gov.

|May 21, 2016

Summary

This summary is machine-generated.

Searching for variable phosphorylation in mass spectrometry does not always increase false positives. This study demonstrates that common database search algorithms can handle phosphoserine and phosphothreonine modifications without significantly impacting false discovery rates.

Keywords:

Bioinformatics Mass spectrometry Peptide spectrum matching Variable modification

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Last Updated: Mar 21, 2026

Oligopeptide Competition Assay for Phosphorylation Site Determination

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Published on: May 18, 2017

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

Published on: April 29, 2022

Identification of Post-translational Modifications of Plant Protein Complexes

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Published on: February 22, 2014

Area of Science:

Proteomics
Biochemistry
Analytical Chemistry

Background:

Mass spectrometry is crucial for identifying proteins and post-translational modifications (PTMs).
Variable PTMs, such as phosphorylation, present challenges in data interpretation.
Concerns exist that searching for variable phosphorylation increases false-positive peptide identifications.

Purpose of the Study:

To investigate whether searching for variable phosphoserine and phosphothreonine modifications increases false-positive matches in peptide tandem mass spectra.
To analyze the impact of variable phosphorylation searches on the false discovery rate (FDR).
To clarify how a popular database search algorithm handles variable phosphorylation.

Main Methods:

Analysis of peptide tandem mass spectra using a database-search algorithm.
Systematic evaluation of search parameters for variable phosphoserine and phosphothreonine.
Examination of the algorithm's search space expansion and FDR.

Main Results:

The search for variable phosphoserine and phosphothreonine does not invariably double the search space.
The inclusion of variable phosphorylation did not unduly impinge upon the FDR in tested scenarios.
A detailed explanation of the algorithm's approach to variable phosphorylation is provided.

Conclusions:

Database search algorithms can effectively interpret spectra with variable phosphorylation without a proportional increase in false positives.
The premise that variable phosphorylation searches inherently double the search space and inflate FDR is not universally true.
This work provides a clearer understanding of variable phosphorylation searching in proteomics.