PXD012565

PXD012565 is an original dataset announced via ProteomeXchange.

Title	INKA, an integrative analysis pipeline for inference of hyperactive phosphokinases in mass spectrometry-based phosphoproteomics data: CRC Organoids
Description	CRC Organoid and corresponding PDX data are part of a larger project that includes proteomeXchange accessions PXD006616, PXD008032, and PXD009995. We present a computational pipeline called Integrative Inferred Kinase Activity (INKA) scoring that integrates the observed abundance of phosphopeptides derived from (i) kinases as a whole, (ii) their kinase activation loop segments, (iii) proteins deduced to be kinase substrates based on prior experimental knowledge of kinase-substrate relationships, and/or (iv) kinase substrates predicted by the sequence motif- and network-based NetworKIN algorithm.
HostingRepository	PRIDE
AnnounceDate	2019-04-18
AnnouncementXML	Submission_2019-04-18_04:11:48.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; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-30 07:57:32	ID requested
⏵ 1	2019-04-18 04:19:50	announced

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]

curator keyword: Technical, Biomedical

submitter keyword: Human, CRC, phosphokinase ranking, label-free, single-shot, phosphoproteomics, PDX, Organoids

Connie Ramona Jimenez
contact affiliation	Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, 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/PXD012565

PRIDE project URI

• PRIDE
  1. PXD012565
     1. Label: PRIDE project
     2. Name: INKA, an integrative analysis pipeline for inference of hyperactive phosphokinases in mass spectrometry-based phosphoproteomics data: CRC Organoids