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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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Updated: Jun 25, 2025

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Advancing Nanomaterial Toxicology Screening Through Efficient and Cost-Effective Quantitative Proteomics.

Tobias Stobernack¹, Nils Dommershausen¹, Víctor Alcolea-Rodríguez^1,2

¹German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany.

|May 30, 2024

Summary

This study presents an advanced tandem mass tag (TMT) labeling protocol for reproducible proteomic analysis in toxicology. The cost-effective TMT method enhances sensitivity for nanomaterial toxicity assessment in lung cells, outperforming label-free quantification (LFQ).

Keywords:

Tandem mass tag (TMT)adverse outcome pathway (AOP)mode of action (MoA)nanomaterials (NMs)new approach methodologies (NAMs)proteomics

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Area of Science:

Proteomics
Toxicology
Nanomaterial Safety

Background:

Proteomic datasets are high-dimensional but face reproducibility issues in toxicology due to variable conditions.
Traditional label-free quantification (LFQ) can be costly and less sensitive for large-scale toxicological screenings.

Purpose of the Study:

To introduce an advanced, cost-effective tandem mass tag (TMT) labeling protocol for improved proteomic analysis in toxicology.
To enhance the sensitivity and reproducibility of toxicological assessments, particularly for nanomaterials.

Main Methods:

Developed an advanced TMT labeling protocol reducing reagent use tenfold and requiring minimal biological material (1 µg).
Applied the protocol to assess the toxicity of nine benchmark nanomaterials (NMs) on A549 lung epithelial cells.
Compared the advanced TMT protocol's performance against traditional label-free quantification (LFQ).

Main Results:

The advanced TMT protocol demonstrated increased reproducibility compared to LFQ.
Despite detecting fewer proteins (2600 vs 3300), the TMT protocol showed superior sensitivity in detecting NM-induced alterations.
LFQ measurements were inadequate for revealing NM toxicity, while the TMT protocol successfully identified it.

Conclusions:

The advanced TMT protocol offers an efficient and cost-effective solution for large-scale toxicological assessments.
This method enables simultaneous evaluation of multiple substances, aiding hazard prioritization and ranking.
The protocol supports the development of New Approach Methodologies (NAMs) in toxicology.