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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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...
Phosphoinositides and PIPs01:42

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.
Different phosphoinositides are synthesized and recruited on the cytosolic face of the plasma membrane. The localization of specific phosphoinositides concentrated in separate membrane...

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Updated: Jul 4, 2026

Oligopeptide Competition Assay for Phosphorylation Site Determination
09:16

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information.

Yunhu Wan1, Diane Cripps, Stefani Thomas

  • 1Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201, USA. ywan@som.umaryland.edu

Journal of Proteome Research
|June 14, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces PhosphoScan, a new method for pinpointing phosphorylation sites on peptides. PhosphoScan significantly improves the accuracy of identifying these critical sites in biological research.

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Oligopeptide Competition Assay for Phosphorylation Site Determination
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10:17

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

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry
  • Proteomics
  • Computational Biology

Background:

  • Phosphorylation is a key post-translational modification regulating numerous cellular processes.
  • Accurate identification of phosphorylation sites is essential for understanding signaling pathways.
  • Multiple phosphorylations on a single peptide complicate site localization.

Purpose of the Study:

  • To develop a robust method for unambiguous phosphorylation site determination in phosphopeptides.
  • To improve the accuracy of phosphopeptide analysis, especially in cases of multiple phosphorylations.
  • To provide a tool that enhances the reliability of phosphoproteomic studies.

Main Methods:

  • Developed a probability-based computational method utilizing MS2/3 pair information.
  • Applied the method to analyze spectral data from synthetic doubly phosphorylated peptides.
  • Compared the performance of the new method against established algorithms like SEQUEST and MASCOT.

Main Results:

  • The developed PhosphoScan method demonstrated superior performance in phosphopeptide localization.
  • Achieved a 63% improvement in phosphopeptide localization compared to SEQUEST.
  • Showed a 57% improvement in phosphopeptide localization compared to MASCOT.

Conclusions:

  • PhosphoScan offers a significant advancement in accurately determining phosphorylation sites.
  • The method effectively addresses the challenges posed by multiple phosphorylations in peptides.
  • This tool is expected to enhance the depth and reliability of phosphoproteomic research.