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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Modifications in the RER01:26

Protein Modifications in the RER

Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal sequences.

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

Published on: May 22, 2018

Using the scan-x Web site to predict protein post-translational modifications.

Michael F Chou1, Daniel Schwartz2

  • 1Department of Genetics, Harvard Medical School, Boston, Massachusetts.

Current Protocols in Bioinformatics
|December 14, 2011
PubMed
Summary

This study introduces scan-x, a web tool for viewing predicted protein acetylation and phosphorylation sites across multiple species. It offers high specificity for post-translational modification analysis in proteomics research.

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Area of Science:

  • Proteomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Proteomic mass spectrometry data reveals extensive post-translational modifications (PTMs) in cellular proteins.
  • Understanding PTMs is crucial for deciphering protein function and cellular regulation.

Purpose of the Study:

  • To present a protocol for utilizing the scan-x website.
  • To enable visualization of predicted protein acetylation and phosphorylation sites.
  • To provide a high-specificity tool for analyzing PTMs in various proteomes.

Main Methods:

  • Utilizing the scan-x web-based platform.
  • Searching for specific proteins within the human, mouse, fly, and yeast proteomes.
  • Viewing predicted acetylation and phosphorylation sites with high specificity.

Main Results:

  • The scan-x website allows for the prediction and viewing of acetylation sites in the human proteome.
  • Predicted phosphorylation sites can be viewed for human, mouse, fly, and yeast proteomes.
  • The protocol requires only a web browser and protein search functionality.

Conclusions:

  • The scan-x tool provides accessible, high-specificity predictions for protein acetylation and phosphorylation.
  • This resource facilitates the study of PTMs across different organisms.
  • The web-based nature ensures broad accessibility for researchers in proteomics and molecular biology.