PXD030450

PXD030450 is an original dataset announced via ProteomeXchange.

Title	Comparative assessment of quantification methods for tumor tissue phosphoproteomics
Description	The choice of quantification method is critical for study design and comparison of cancer phosphoproteomes. We comparatively assessed label-free quantification (LFQ), spike-in-SILAC (stable isotope labeling of amino acids in cell culture) and tandem mass tag (TMT) labeling techniques for quantitative phosphoproteome analysis in tumor tissues. Using ovarian cancer tissue as an example, our study establishes a resource for the design and analysis of quantitative phosphoproteomics studies in cancer research and diagnosis. TMT provided the lowest accuracy and the highest precision and robustness across different phosphosite abundances and matrices (cell culture versus tumor tissue). Spike-in-SILAC offered the best compromise between these features, but was limited by low phosphosite coverage. LFQ provided the lowest precision, but the highest number of phosphosite identifications. Spike-in-SILAC and LFQ were susceptible to matrix effects arising from different sample types. Analysis based on match between run (MBR) improved phosphosite coverage across technical replicates in LFQ and spike-in-SILAC, but further reduced the precision and robustness of quantification.
HostingRepository	PRIDE
AnnounceDate	2022-08-09
AnnouncementXML	Submission_2022-08-09_09:41:11.065.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	yang zhang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-16 11:49:05	ID requested
⏵ 1	2022-08-09 09:41:11	announced

Zhang Y, Dreyer B, Govorukhina N, Heberle AM, Kon, č, arevi, ć S, Krisp C, Opitz CA, Pf, ä, nder P, Bischoff R, Schl, ü, ter H, Kwiatkowski M, Thedieck K, Horvatovich PL, Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics. Anal Chem, 94(31):10893-10906(2022) [pubmed]

submitter keyword: phosphoproteomics, tissue, ovarian cancer, quantification

Peter L. Horvatovich
contact affiliation	Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands.
contact email	p.l.horvatovich@rug.nl
lab head
yang zhang
contact affiliation	Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
contact email	wdyangzh@hotmail.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/2022/08/PXD030450

PRIDE project URI

• PRIDE
  1. PXD030450
     1. Label: PRIDE project
     2. Name: Comparative assessment of quantification methods for tumor tissue phosphoproteomics