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Related Concept Videos

Proteomics01:33

Proteomics

7.4K
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...
7.4K

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Updated: Jul 20, 2025

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
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TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

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Tissue proteomics repositories for data reanalysis.

Rafael Stroggilos1, Aggeliki Tserga1, Jerome Zoidakis1

  • 1Biomedical Research Foundation, Academy of Athens, Department of Biotechnology, Athens, Greece.

Mass Spectrometry Reviews
|August 3, 2023
PubMed
Summary

Proteomics data repositories are growing, but half of human tissue datasets lack essential metadata for reuse. Improving metadata submission is crucial for advancing systems biology research.

Keywords:
PRIDEProteomeXchangedata repositoriesmass spectrometryproteomicstissue

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Area of Science:

  • Proteomics
  • Systems Biology
  • Bioinformatics

Background:

  • Proteomics repositories have existed for nearly two decades, accumulating vast mass spectrometry data.
  • The field is maturing with standardized terminology and file formats, integrating proteomics into systems biology.
  • ProteomeXchange is a consortium of proteomics data repositories.

Purpose of the Study:

  • To evaluate public human tissue datasets in ProteomeXchange repositories from 2015-2022.
  • To map existing information and assess the reusability of these datasets.
  • To identify challenges and opportunities for improving proteomics data sharing.

Main Methods:

  • Searched, collected, and evaluated public human tissue datasets categorized as "complete" within ProteomeXchange.
  • Analyzed data representation by disease category (cancers, neuronal, cardiovascular).
  • Assessed dataset annotations and metadata completeness for replicability.

Main Results:

  • Human tissue data comprised 10-25% of total submissions, with cancers most represented.
  • Approximately 50% of reviewed datasets lacked sufficient metadata for direct analysis replication.
  • Proteomics repositories have grown significantly in size and functionality over the past seven years.

Conclusions:

  • Significant challenges remain in ensuring the reusability of proteomics data due to incomplete metadata.
  • Increased community awareness and adoption of metadata standards like the 'mage-tab' file format are necessary.
  • Securing detailed metadata for all submissions is the next critical milestone for proteomics repositories.