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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...

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

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Data management and data integration in the HUPO plasma proteome project.

Gilbert S Omenn1

  • 1Departments of Medicine and Genetics, Center for Computational Medicine and Bioinformatics, Medical School and School of Public Health, University of Michigan, Ann Arbor, MI, USA. gomenn@umich.edu

Methods in Molecular Biology (Clifton, N.J.)
|November 11, 2010
PubMed
Summary

The Human Plasma Proteome Project (HPPP) established a core dataset of 3,020 human plasma proteins. This work provides a foundation for comparing proteomes in health and disease.

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Area of Science:

  • Proteomics
  • Human Biology
  • Bioinformatics

Background:

  • The Human Plasma Proteome Project (HPPP) is an international effort by the Human Proteome Organisation (HUPO).
  • Previous work includes a 2005 Proteomics special issue and a book detailing the pilot phase.
  • Data management challenges involve integrating complex, dynamic serum and plasma specimen data.

Purpose of the Study:

  • To assemble a representative core dataset of human plasma protein identifications.
  • To overcome ambiguity and redundancy in contributed identifications and protein sequence databases.
  • To make human plasma proteome data available for comparative analysis in health and disease.

Main Methods:

  • Assembled a core dataset of 3,020 protein identifications from participating laboratories.
  • Managed data through collection, integration, analysis, and dissemination.
  • Utilized Proteome Xchange for linking datasets to EBI/PRIDE and Tranche/Proteome Commons.org for data sharing.

Main Results:

  • Generated a core dataset of 3,020 protein identifications, addressing data heterogeneity.
  • Provided results with alternative thresholds, offering a range of protein identification numbers.
  • Submitted data to EBI/PRIDE and ISB/PeptideAtlas for accessibility.

Conclusions:

  • The HPPP has created a valuable resource for human plasma proteome research.
  • Standardized data submission and sharing through Proteome Xchange enhances data accessibility.
  • These datasets facilitate comparative proteomic studies across different biological states and conditions.