PXD020828-1

PXD020828 is an original dataset announced via ProteomeXchange.

Title	16-plex isobaric mass tags enable streamlined proteomics-based drug mechanism-of-action studies
Description	Multiplexed quantitative proteomics enables the development of complex workflows for studying the mechanisms by which small molecule drugs interact with the proteome such as thermal proteome profiling (TPP) or multiplexed proteome dynamics profiling (mPDP). TPP measures changes in protein thermal stability in response to drug treatment and thus informs on direct targets and downstream regulation events, while the mPDP approach enables the discovery of regulated protein synthesis and degradation events caused by small molecules and other perturbations. The mass tags available for multiplexed proteomics have thus far limited the efficiency and sensitivity with which such experiments could be performed. Here we evaluate a new generation of 16-plex isobaric mass tags and demonstrate similar sensitivity and accuracy of quantification as the previously described TMT reagents. The TMT16 tags enabled the sensitive and time efficient identification of staurosporine targets in HepG2 cell extracts by recording full thermal denaturation/aggregation profiles of vehicle and compound treated samples in a single mass spectrometry experiment. In 2D-TPP experiments, isothermal titration over 7 concentrations per temperature enabled comprehensive selectivity profiling of staurosporine with EC50 values for kinase targets tightly matching to the kinobeads gold standard assay. Finally, we demonstrate time and condition-based multiplexing of dynamic SILAC labeling experiments to delineate proteome-wide effects of the molecular glue Indisulam on synthesis and degradation rates.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_13:34:50.099.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Toby Mathieson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; 6x(13)C; methionine oxidation with neutral loss of 64 Da; 6x(13)C; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-10 09:23:28	ID requested
⏵ 1	2024-10-07 13:34:51	announced

10.1021/acs.jproteome.0c00900;

Zinn N, Werner T, Doce C, Mathieson T, Boecker C, Sweetman G, Fufezan C, Bantscheff M, Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags. J Proteome Res, 20(3):1792-1801(2021) [pubmed]

submitter keyword: TMTPro, isobaric labeling, 2D-TPP,TMT, mPDP, TPP

Marcus Bantscheff
contact affiliation	Cellzome
contact email	marcus.x.bantscheff@gsk.com
lab head
Toby Mathieson
contact affiliation	Cellzome - a GSK company Meyerhofstrasse 1, 69117 HEIDELBERG
contact email	toby.j.mathieson@gsk.com
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/2021/02/PXD020828

PRIDE project URI

• PRIDE
  1. PXD020828
     1. Label: PRIDE project
     2. Name: 16-plex isobaric mass tags enable streamlined proteomics-based drug mechanism-of-action studies