PXD001374

PXD001374 is an original dataset announced via ProteomeXchange.

Title	Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling
Description	Label-free quantification is a powerful method for studying cellular protein phosphorylation dynamics. However, whether current data normalization methods achieve sufficient accuracy has not been examined systematically. Here, we demonstrate that a large uni-directional shift in the phosphopeptide abundance distribution is problematic for global median centering and quantile-based normalizations and may mislead the biological conclusion from unlabeled phosphoproteome data. Instead, we present a novel normalization strategy, named pairwise normalization, which is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of pairwise normalization was validated by statistical methods, western blotting analysis, and by bioinformatics analysis. In addition, we demonstrate that the choice of normalization method influences the downstream analyses of the data and perceived pathway activities. Furthermore, we demonstrate that the developed normalization method, combined with pathway analysis algorithms, revealed a novel biological synergism between Ras signalling and PP2A inhibition by CIP2A.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_03:58:38.089.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Susumu Imanishi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-10-02 00:25:57	ID requested
1	2015-08-24 03:25:06	announced
⏵ 2	2024-10-22 03:58:42	announced	2024-10-22: Updated project metadata.

10.1038/srep13099;

Kauko O, Laajala TD, Jumppanen M, Hintsanen P, Suni V, Haapaniemi P, Corthals G, Aittokallio T, Westermarck J, Imanishi SY, Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling. Sci Rep, 5():13099(2015) [pubmed]

ProteomeXchange project tag: deep learning, benchmarking, machine learning

curator keyword: Biomedical

submitter keyword: Mascot,Phosphoproteomics, CIP2A, HeLa, Okadaic acid, RAS, SimSpectraST, LC-MS/MS

Susumu Y. Imanishi
contact affiliation	Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Finland
contact email	susumu.imanishi@btk.fi
lab head
Susumu Imanishi
contact affiliation	Meijo University
contact email	susima@meijo-u.ac.jp
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/2015/08/PXD001374

PRIDE project URI

• PRIDE
  1. PXD001374
     1. Label: PRIDE project
     2. Name: Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling