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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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Protein Complexes with Interchangeable Parts01:57

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Protein Complexes with Interchangeable Parts

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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Updated: Jan 11, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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The ProteomeXchange consortium in 2026: making proteomics data FAIR.

Eric W Deutsch1, Nuno Bandeira2,3,4, Yasset Perez-Riverol5

  • 1Institute for Systems Biology, Seattle WA 98109, United States.

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The ProteomeXchange consortium standardizes mass spectrometry (MS)-based proteomics data sharing. Recent developments show accelerated data submissions and increased data reuse, with future plans for controlled-access data and non-MS approaches.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Science

Background:

  • The ProteomeXchange consortium was founded to standardize open data practices in mass spectrometry (MS)-based proteomics.
  • Six global databases (PRIDE, PeptideAtlas, MassIVE, jPOST, iProX, Panorama Public) form the consortium.

Purpose of the Study:

  • To report on the key developments within ProteomeXchange over the past three years.
  • To highlight advancements in data submission, standardization, and data reuse.

Main Methods:

  • Analysis of data submission statistics from ProteomeXchange member databases.
  • Review of improvements in supporting Proteomics Standards Initiative standards (e.g., Universal Spectrum Identifiers, SDRF-Proteomics).
  • Assessment of data reuse trends and the application of machine learning in proteomics data analysis.

Main Results:

  • Data submissions to ProteomeXchange have accelerated, with 47% of the total 64,330 datasets submitted in the last three years (by June 2025).
  • Enhanced support for Proteomics Standards Initiative standards has been implemented.
  • Increased data reuse is evident, including reanalyses and novel machine learning applications.

Conclusions:

  • ProteomeXchange continues to grow, facilitating open data practices in MS-based proteomics.
  • Future efforts will focus on resources for controlled-access human proteomics data and non-MS proteomics approaches.