PXD008032

PXD008032 is an original dataset announced via ProteomeXchange.

Title	Differential activity of treatment with protein kinase inhibitors on tumor phosphotyrosine profiles in patients with advanced cancer
Description	Mass spectrometry-based phosphoproteomics of tumor tissue lysates provides a potential personalized medicine approach based on its ability to identify activated signaling pathways and novel drug targets. We performed a pilot study (NCT01636908) to determine the effect of protein kinase inhibitors (PKIs) on tyrosine-(pTyr)-phosphoproteomic profiles of serial tumor biopsies in patients with advanced cancer. Tumor needle biopsies were analyzed from 31 patients with advanced cancer before and after 2 weeks treatment with sorafenib (SOR), erlotinib (ERL), dasatinib (DAS), vemurafenib (VEM), sunitinib (SUN) or everolimus (EVE). pTyr-Phosphoproteomics of pre- and on-treatment biopsies was performed by phosphotyrosine immunoprecipitation followed by LC-MS/MS.
HostingRepository	PRIDE
AnnounceDate	2020-02-17
AnnouncementXML	Submission_2020-02-17_01:32:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sander Piersma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-24 07:15:17	ID requested
1	2019-04-18 04:44:32	announced
⏵ 2	2020-02-17 01:32:30	announced	2020-02-17: Updated publication reference for PubMed record(s): 32024067, 30979792.

Beekhof R, van Alphen C, Henneman AA, Knol JC, Pham TV, Rolfs F, Labots M, Henneberry E, Le Large TY, de Haas RR, Piersma SR, Vurchio V, Bertotti A, Trusolino L, Verheul HM, Jimenez CR, INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases. Mol Syst Biol, 15(4):e8250(2019) [pubmed]

Labots M, Pham TV, Honeywell RJ, Knol JC, Beekhof R, de Goeij-de Haas R, Dekker H, Neerincx M, Piersma SR, van der Mijn JC, van der Peet DL, Meijerink MR, Peters GJ, van Grieken NCT, Jim, é, nez CR, Verheul HMW, Kinase Inhibitor Treatment of Patients with Advanced Cancer Results in High Tumor Drug Concentrations and in Specific Alterations of the Tumor Phosphoproteome. Cancers (Basel), 12(2):(2020) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Human, Tyrosine kinase, protein kinase inhibitor, label-free, single-shot, phosphoproteomics

Connie Ramona Jimenez
contact affiliation	OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
contact email	c.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliation	OncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact email	s.piersma@vumc.nl
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/2019/04/PXD008032

PRIDE project URI

• PRIDE
  1. PXD008032
     1. Label: PRIDE project
     2. Name: Differential activity of treatment with protein kinase inhibitors on tumor phosphotyrosine profiles in patients with advanced cancer