PXD020248

PXD020248 is an original dataset announced via ProteomeXchange.

Title	Comparison of LFQ and TMT-based quantitative proteomics towards toxicology research
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:17:05.711.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhipeng Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-07 16:29:07	ID requested
1	2021-03-04 12:57:58	announced
⏵ 2	2024-10-22 05:17:06	announced	2024-10-22: Updated project metadata.

10.1016/j.tox.2020.152652;

Wang Z, Karkossa I, Gro, ß, kopf H, Rolle-Kampczyk U, Hackerm, ü, ller J, von Bergen M, Schubert K, Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP. Toxicology, 448():152652(2021) [pubmed]

submitter keyword: toxicoproteomics, Benzo[a]pyrene, tandem mass tag (TMT), label free-quantification (LFQ), HepG2

Kristin Schubert
contact affiliation	Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany
contact email	kristin.schubert@ufz.de
lab head
Zhipeng Wang
contact affiliation	Helmholtz Centre for Environmental Research
contact email	zhipeng.wang@ufz.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD020248

PRIDE project URI

• PRIDE
  1. PXD020248
     1. Label: PRIDE project
     2. Name: Comparison of LFQ and TMT-based quantitative proteomics towards toxicology research