Proteomics

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Comparison of LFQ and TMT-based quantitative proteomics towards toxicology research

ABSTRACT: Here, we aimed to compare two of the most commonly used global proteomics strategies, label-free quantification (LFQ) and tandem mass tag-based quantification (TMT) to identify the most suitable tool for toxicology research questions on the systemic level. Using a biological case study of HepG2 exposure to benzo[a]pyrene (BaP), we uncovered the advantages and limitations of the two strategies from the view of proteome coverage, fold changes, significant numbers of proteins, and pathway alterations.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hepatocyte, Liver

SUBMITTER: Zhipeng Wang  

LAB HEAD: Kristin Schubert

PROVIDER: PXD020248 | Pride | 2020-12-23

REPOSITORIES: Pride

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20191219_HepG2_sp3_LFQ_BaP_BP1_F1.raw Raw
20191219_HepG2_sp3_LFQ_BaP_BP1_F2.raw Raw
20191219_HepG2_sp3_LFQ_BaP_BP2_F1.raw Raw
20191219_HepG2_sp3_LFQ_BaP_BP2_F2.raw Raw
20191219_HepG2_sp3_LFQ_BaP_BP3_F1.raw Raw
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Publications

Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP.

Wang Zhipeng Z   Karkossa Isabel I   Großkopf Henning H   Rolle-Kampczyk Ulrike U   Hackermüller Jörg J   von Bergen Martin M   Schubert Kristin K  

Toxicology 20201202

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  ...[more]

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