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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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Optimized Protocol for the Extraction of Proteins from the Human Mitral Valve
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Predicting protein post-translational modifications using meta-analysis of proteome scale data sets.

Daniel Schwartz1, Michael F Chou, George M Church

  • 1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. dschwartz@genetics.med.harvard.edu

Molecular & Cellular Proteomics : MCP
|November 1, 2008
PubMed
Summary

This study introduces a new strategy to predict protein post-translational modifications. The method improves prediction accuracy for phosphorylation and acetylation sites across multiple organisms.

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Last Updated: Jun 28, 2026

Optimized Protocol for the Extraction of Proteins from the Human Mitral Valve
09:13

Optimized Protocol for the Extraction of Proteins from the Human Mitral Valve

Published on: June 14, 2017

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Area of Science:

  • Proteomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Protein post-translational modifications (PTMs) are crucial for biological regulation.
  • High-throughput techniques are rapidly increasing the discovery of PTMs.
  • Utilizing vast sequence data for PTM prediction is essential.

Purpose of the Study:

  • To develop a general strategy for predicting various PTMs in multiple organisms.
  • To identify phosphorylation and lysine acetylation motifs.
  • To globally predict potential modification sites.

Main Methods:

  • Utilized the motif-x program to identify phosphorylation and lysine acetylation motifs.
  • Employed a new tool, scan-x, to scan proteomic data for modification sites.
  • Performed 10-fold cross-validation to assess prediction accuracy.

Main Results:

  • The developed strategy improved phosphoprediction sensitivity and specificity compared to existing tools.
  • Successfully predicted potential phosphorylation and lysine acetylation sites across yeast, fly, mouse, and human.
  • Identified conserved known and novel kinase motifs, indicating evolutionary conservation.

Conclusions:

  • The new strategy offers a robust approach for predicting PTMs.
  • The findings highlight the evolutionary conservation of kinase motifs.
  • This method aids in understanding the regulatory roles of PTMs through sequence data analysis.