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Related Concept Videos

Phosphorylation01:02

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...
Phosphorylation01:02

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...
Protein Kinases and Phosphatases02:54

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 Phosphatases02:54

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...

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Related Experiment Video

Updated: May 27, 2026

Oligopeptide Competition Assay for Phosphorylation Site Determination
09:16

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

Universal and confident phosphorylation site localization using phosphoRS.

Thomas Taus1, Thomas Köcher, Peter Pichler

  • 1Research Institute of Molecular Pathology, Dr. Bohrgasse 7, A-1030 Vienna, Austria.

Journal of Proteome Research
|November 15, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new algorithm for pinpointing phosphorylation sites in peptides using tandem mass spectrometry. The developed software accurately identifies over 3000 phosphorylation sites in biological samples.

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An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation
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An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

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Related Experiment Videos

Last Updated: May 27, 2026

Oligopeptide Competition Assay for Phosphorylation Site Determination
09:16

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation
07:45

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

Published on: June 6, 2022

Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Phosphorylation is a key post-translational modification regulating protein function.
  • Accurate identification of phosphorylation sites is crucial for understanding cellular signaling pathways.
  • Existing methods for phosphorylation site localization have limitations in accuracy and scalability.

Purpose of the Study:

  • To develop and validate a novel algorithm for the accurate assignment of phosphorylation sites in peptides.
  • To improve the precision and reliability of phosphorylation site localization using tandem mass spectrometry data.
  • To assess the algorithm's performance against existing tools and its applicability to large-scale phosphoproteomic studies.

Main Methods:

  • Utilized tandem mass spectrometry data and peptide sequences to calculate site probabilities.
  • Optimized scoring parameters using synthetic phosphopeptides and various fragmentation techniques.
  • Implemented a novel peak extraction approach with adaptable peak depths for spectrum regions.
  • Validated the algorithm using synthetic phosphopeptide mixtures and analyzed phosphopeptides from a biological sample.

Main Results:

  • The algorithm demonstrated high precision in phosphorylation site localization, exceeding expectations based on probability cutoffs.
  • Successfully localized over 3000 nonredundant phosphorylation sites in a complex biological sample.
  • The novel peak extraction method enhanced data matching accuracy.
  • Empirical precision was found to be higher than predicted by the probability cutoff.

Conclusions:

  • The developed algorithm provides a robust and accurate method for phosphorylation site assignment.
  • The software demonstrates practical applicability for large-scale phosphoproteomic analyses.
  • The findings suggest potential improvements over existing phosphorylation site localization tools like Ascore.