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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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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.
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Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets.

Andrew F Jarnuczak1, Juan Antonio Vizcaíno1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

Current Protocols in Bioinformatics
|September 14, 2017
PubMed
Summary

The ProteomeXchange (PX) Consortium unifies global mass spectrometry proteomics data repositories. It standardizes data submission and access through common guidelines and unique identifiers, enhancing research accessibility.

Keywords:
PRIDE databasedata repositorymass spectrometryproteomics

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Science

Background:

  • Mass spectrometry (MS)-based proteomics generates vast datasets.
  • Decentralized repositories hinder data accessibility and standardization.
  • A unified framework is needed for global proteomics data sharing.

Purpose of the Study:

  • To introduce the ProteomeXchange (PX) Consortium as a unifying framework for proteomics data repositories.
  • To outline the standardization protocols for data submission and dissemination.
  • To guide researchers on data submission and access through the PX portal.

Main Methods:

  • Establishment of a consortium with leading MS-based proteomics repositories (PRIDE, PeptideAtlas/PASSEL, MassIVE, jPOST).
  • Implementation of common data submission guidelines and metadata requirements.
  • Development of a common identifier space with unique accession numbers (PXD).

Main Results:

  • Standardized submission and dissemination of public proteomics data worldwide.
  • Public accessibility of datasets upon publication release.
  • A central portal (ProteomeCentral) for searching all member datasets.

Conclusions:

  • The PX Consortium effectively unifies global proteomics data repositories.
  • Standardized protocols enhance data sharing and accessibility for the scientific community.
  • ProteomeCentral facilitates efficient searching of publicly available proteomics datasets.