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Proteomics

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...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Related Experiment Video

Updated: May 26, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

A novel method to select Reference Proteomes in UniProt.

Pedro Raposo¹, Juan Sebastian Martinez Marin¹, Gyuri Kim^2,3

¹European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Biorxiv : the Preprint Server for Biology

|May 25, 2026

Summary

This summary is machine-generated.

A new pipeline selects optimal Reference Proteomes for cellular organisms, ensuring comprehensive species representation in UniProt. This approach enhances the UniProt Knowledgebase by increasing proteome coverage and reducing protein redundancy.

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

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Last Updated: May 26, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Area of Science:

Bioinformatics
Genomics
Proteomics

Background:

Genome sequencing advancements generate vast amounts of proteomic data for repositories like UniProt.
Managing this data deluge requires a systematic approach to select representative proteomes.

Purpose of the Study:

To develop and implement a novel pipeline for selecting optimal Reference Proteomes for cellular organisms.
To ensure UniProt's proteome data is concise, representative, and sustainably managed.

Main Methods:

A clustering algorithm utilizing MMseqs2 was employed to identify the minimum set of Reference Proteomes maximizing protein space representation.
Viral Reference Proteomes were aligned with the International Committee on Taxonomy of Viruses' exemplar genome set.

Main Results:

The pipeline successfully increased the number of Reference Proteomes by 36%, covering 34% more species in the Tree of Life.
The overall number of proteins in the UniProt Knowledgebase was reduced by 43% through this selection process.

Conclusions:

The implemented pipeline provides a sustainable method for managing and curating proteomic data in UniProt.
This approach results in a more concise and representative UniProt Knowledgebase, improving data accessibility and utility.