Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1016/j.tox.2020.152652
Licence creative commons licence
Title (Primary) Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP
Author Wang, Z.; Karkossa, I.; Großkopf, H.; Rolle-Kampczyk, U.; Hackermüller, J. ORCID logo ; von Bergen, M.; Schubert, K.
Source Titel Toxicology
Year 2020
Department MOLSYB
Volume 448
Page From art. 152652
Language englisch
Supplements https://ars.els-cdn.com/content/image/1-s2.0-S0300483X20302912-mmc1.pdf
https://ars.els-cdn.com/content/image/1-s2.0-S0300483X20302912-mmc2.xlsx
Keywords toxicoproteomics; hepatocytes; BaP; AhR; mode of action
Abstract

The application of quantitative proteomics provides a new and promising tool for standardized toxicological research. However, choosing a suitable quantitative method still puzzles many researchers because the optimal method needs to be determined.

In this study, we investigated the advantages and limitations of two of the most commonly used global quantitative proteomics methods, namely label-free quantitation (LFQ) and tandem mass tags (TMT). As a case study, we exposed hepatocytes (HepG2) to the environmental contaminant benzo[a]pyrene (BaP) using a concentration of 2 µM. Our results revealed that both methods yield a similar proteome coverage, in which for LFQ a wider range of fold changes was observed but with less significant p-values compared to TMT. We detected 37 and 47 significantly enriched pathways by LFQ and TMT, respectively, with 17 overlapping pathways.

To define the minimally required effort in proteomics as a benchmark, we artificially reduced the LFQ, and TMT data sets stepwise and compared the pathway enrichment. Thereby, we found that fewer proteins are necessary for detecting significant enrichment of pathways in TMT compared to LFQ, which might be explained by the higher reproducibility of the TMT data that was observed.

In summary, we showed that the TMT approach is the preferable one when investigating toxicological questions because it offers a high reproducibility and sufficient proteome coverage in a comparably short time.

Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=23988
Wang, Z., Karkossa, I., Großkopf, H., Rolle-Kampczyk, U., Hackermüller, J., von Bergen, M., Schubert, K. (2020):
Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP
Toxicology 448 , art. 152652 10.1016/j.tox.2020.152652