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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...

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Related Experiment Video

Updated: Aug 6, 2025

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping.

Aileen Bahl¹, Celine Ibrahim¹, Kristina Plate¹

¹Department of Chemicals and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany.

Journal of Cheminformatics

|March 20, 2023

Summary

A new tool, PROTEOMAS, enables harmonized analysis of public proteomics data for regulatory toxicology. This supports developing alternative testing strategies and understanding substance mechanisms of action, reducing animal testing.

Keywords:

Adverse outcome pathways (AOP)FAIR data Harmonized proteomics data analysis Meta-analysis Mode-of-action (MoA)Nanomaterials Proteomics

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Last Updated: Aug 6, 2025

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

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Published on: January 10, 2025

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

Area of Science:

Toxicology
Proteomics
Computational Biology

Background:

Regulatory toxicology heavily relies on animal testing, necessitating alternative strategies.
Omics methods, particularly proteomics, offer potential for understanding substance mechanisms but face data integration challenges.
Publicly available proteomics datasets are underutilized due to inconsistent data processing.

Purpose of the Study:

To introduce PROTEOMAS, a workflow for harmonized meta-analysis of public proteomics data.
To facilitate the integration of proteomics into regulatory toxicology and support the development of Adverse Outcome Pathways (AOPs).
To enhance transparency and reliability in analyzing proteomic data for regulatory decision-making.

Main Methods:

Development of the PROTEOMAS workflow for standardized proteomic data analysis.
Adherence to OECD Omics Reporting Framework guidelines.
Meta-analysis of 25 proteomic datasets investigating nanomaterial lung toxicity as a case study.

Main Results:

Demonstrated robustness and reliability of the PROTEOMAS workflow through comparison with original study findings.
Successful meta-analysis of diverse proteomic datasets, yielding insights into toxicological effects.
The workflow adheres to FAIR data principles, promoting data accessibility and reusability.

Conclusions:

PROTEOMAS provides a robust solution for meta-analysis of proteomic data, advancing alternative testing strategies in toxicology.
The tool contributes to understanding substance mechanisms of action and developing AOPs.
Standardized analysis of proteomics data supports regulatory toxicology and reduces reliance on animal experiments.