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Related Concept Videos

Proteomics01:33

Proteomics

8.6K
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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Toxic Reactions: Overview01:26

Toxic Reactions: Overview

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When toxic substances penetrate the human body, they disseminate to various tissues, undergoing metabolic changes. This process yields reactive metabolites that may covalently bind with specific target molecules, resulting in toxicity.
Toxicity falls into two primary categories: local and systemic.
Local toxicity appears at the exposure site, such as protein denaturation caused by caustic substances.
In contrast, systemic toxicity requires the toxic agent's absorption and distribution,...
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The Proteasome01:13

The Proteasome

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Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
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Updated: Oct 26, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Proteomics in systems toxicology.

Carolina Madeira1, Pedro M Costa1

  • 1UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal.

Advances in Protein Chemistry and Structural Biology
|August 3, 2021
PubMed
Summary
This summary is machine-generated.

Proteomics offers a realistic view of toxic effects by analyzing proteins, the end products of gene expression. This whole-proteome approach advances Systems Toxicology for predictive modeling of adverse outcomes.

Keywords:
Adverse outcome pathwaysBioinformaticsGene expressionMass spectrometryMolecular initiating eventsOmicsProteoformProteomeToxicogenomicsToxicoproteomics

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Area of Science:

  • Toxicology
  • Proteomics
  • Systems Biology

Background:

  • Proteins, as the end products of gene expression, provide a more direct and realistic measure of toxicopathic effects and individual susceptibility compared to genes or metabolites.
  • Traditional toxicology often focuses on single endpoints, which can be limited by inter-individual variability.
  • The field of proteomics enables a shift towards comprehensive, whole-proteome screening.

Purpose of the Study:

  • To highlight the advantages of using proteomics in toxicological risk assessment.
  • To introduce the concept of protein-centric adverse outcome pathways (AOPs) within Systems Toxicology.
  • To discuss the potential of advanced proteomics techniques for future toxicological research.

Main Methods:

  • Utilizing proteomics for whole-proteome screening instead of narrow, single-endpoint analyses.
  • Identifying molecular initiating events (MIEs) and AOPs through protein-centric approaches.
  • Leveraging advances in mass spectrometry, bioinformatics, and protein databases.

Main Results:

  • Proteomics provides a more realistic perspective on toxicopathic effects and susceptibility by analyzing proteins.
  • The development of protein-centric AOPs is crucial for advancing Systems Toxicology.
  • Proteomics facilitates predictive modeling of toxicological pathways.

Conclusions:

  • Proteomics represents a significant advancement in risk assessment, moving beyond traditional methods.
  • Systems Toxicology, powered by proteomics and AOPs, is the future of next-generation toxicology.
  • Technological progress in proteomics opens new avenues for mechanistic and effects-oriented toxicological research across various fields.