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Related Concept Videos

Proteomics01:33

Proteomics

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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...
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Related Experiment Video

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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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Cross-Species PTM Mapping from Phosphoproteomic Data.

Rima Chaudhuri1, Jean Yee Hwa Yang2

  • 1Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia. rima.chaudhuri@sydney.edu.au.

Methods in Molecular Biology (Clifton, N.J.)
|February 3, 2017
PubMed
Summary

A new tool, PhosphOrtholog, enables cross-species mapping of novel protein post-translational modification (PTM) sites using mass spectrometry data. This advances understanding of conserved, functional PTMs critical for cell signaling.

Keywords:
Cross-speciesPTM site mappingPost-translational modification (PTM)Web application

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Area of Science:

  • Molecular Biology
  • Proteomics
  • Bioinformatics

Background:

  • Protein post-translational modifications (PTMs) are vital for cellular signal transduction.
  • Identifying evolutionarily conserved PTMs is key to understanding fundamental cell signaling.
  • High-throughput mass spectrometry (MS) generates large-scale, cross-species PTM datasets.

Purpose of the Study:

  • To develop a tool for accurate cross-species comparison of both annotated and novel PTM sites.
  • To overcome limitations of existing tools that rely on pre-annotated orthologous sites.
  • To facilitate the identification of conserved PTMs from experimental MS data across species.

Main Methods:

  • Development of an automated, web-based tool named PhosphOrtholog.
  • Utilizes high-throughput MS-based experimental data from diverse species.
  • Does not require pre-existing PTM databases for mapping orthologous sites.

Main Results:

  • PhosphOrtholog accurately maps annotated and novel orthologous PTM sites.
  • Enables cross-species mapping of PTMs, including newly identified sites.
  • Facilitates analysis of large-scale phosphoproteomics data.

Conclusions:

  • PhosphOrtholog enhances the identification of evolutionarily conserved PTMs across species.
  • This tool expands the knowledgebase of functional PTMs influencing biological processes.
  • Provides a method to map novel PTM sites from cross-species phosphoproteomics data.