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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...

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Related Experiment Video

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Oligopeptide Competition Assay for Phosphorylation Site Determination
09:16

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

Confident phosphorylation site localization using the Mascot Delta Score.

Mikhail M Savitski1, Simone Lemeer, Markus Boesche

  • 1Cellzome AG, Heidelberg, Germany.

Molecular & Cellular Proteomics : MCP
|November 9, 2010
PubMed
Summary

We introduce the Mascot Delta Score (MD-score), a simple and effective method for accurately localizing phosphorylation sites in proteomic research. This new tool offers comparable sensitivity and specificity to existing methods, enhancing phosphoproteome analysis.

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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Last Updated: Jun 6, 2026

Oligopeptide Competition Assay for Phosphorylation Site Determination
09:16

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Phosphorylation analysis is crucial in proteomics.
  • Accurate phosphosite localization remains a significant challenge.
  • Existing methods like Ascore have limitations.

Purpose of the Study:

  • To validate the Mascot Delta Score (MD-score) for phosphosite localization.
  • To compare the MD-score's performance against the Ascore.
  • To assess the MD-score's utility across different fragmentation methods.

Main Methods:

  • Evaluation of the MD-score using liquid chromatography-tandem mass spectrometry (LC-MS/MS) data.
  • Testing the MD-score with 180 synthesized phosphopeptides with known phosphorylation sites.
  • Analysis across various common fragmentation techniques (HCD, ETD, CID, MSA).

Main Results:

  • The MD-score demonstrates high sensitivity and specificity for phosphosite localization, comparable to Ascore.
  • Higher energy collision induced dissociation (HCD) with an Orbitrap analyzer and electron transfer dissociation (ETD) in ion traps showed superior performance.
  • MD-score thresholds were stable across replicate analyses and outperformed Ascore for tyrosine phosphorylation.

Conclusions:

  • The MD-score is a practical and computationally simple method for confident phosphosite localization.
  • MD-score performance is influenced by fragmentation technique, with HCD and ETD being highly effective.
  • The study provides resources for benchmarking and developing future localization software.