PXD009477-3

PXD009477 is an original dataset announced via ProteomeXchange.

Title	Phosphoroteomics analysis of ALK signaling in neuroblastoma cells
Description	We used mass spectrometry-based proteomics to unravel anaplastic lymphoma kinase (ALK) signaling in the ALK and MYCN amplified neuroblastoma cell line, NB1. We specifically measured the ALK phosphoproteome upon siRNA depletion of ALK and upon ALK inhibition using the ALK-targeting small-molecule inhibitor lorlatinib. For quantitative phosphoproteomics we used a tandem mass tag (TMT)-based approach. Conditions for the TMT 11-plex setup is specified below. For each siRNA depletion experiment, NB1 cells were treated with siRNA (80 nM; as specified below) for 48 hours prior to stimulation with 0.1% DMSO for 30 minutes. For inhibitor treatment, NB1 cells were treated for 30 minutes with either 10 microM or 10 nM lorlatinib. The experimental treatment conditions and TMT11-plex labeling are specified below: 126: siControl replicate 1, 0.1% DMSO 127N: siControl replicate 2, 0.1% DMSO 127C: siControl replicate 3, 0.1% DMSO 128N: siALK sequence 1, 0.1% DMSO 128C: siALK sequence 2, 0.1% DMSO 129N: siALK mix of sequence 1 and 2, 0.1% DMSO 129C: 10 microM lorlatinib replicate 1 130N: 10 microM lorlatinib replicate 2 130C: 10 microM lorlatinib replicate 3 131N: 10 nM lorlatinib replicate 1 131C: 10 nM lorlatinib replicate 2
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:44:30.402.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kristina Bennet Emdal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-04-12 02:06:39	ID requested
1	2018-11-21 13:02:01	announced
2	2020-11-17 07:47:36	announced	2020-11-17: Updated publication reference for PubMed record(s): 30459283.
⏵ 3	2024-10-22 04:44:38	announced	2024-10-22: Updated project metadata.

Emdal KB, Pedersen AK, Bekker-Jensen DB, Lundby A, Claeys S, De Preter K, Speleman F, Francavilla C, Olsen JV, Integrated proximal proteomics reveals IRS2 as a determinant of cell survival in ALK-driven neuroblastoma. Sci Signal, 11(557):(2018) [pubmed]

10.1126/scisignal.aap9752;

curator keyword: Biomedical

submitter keyword: LC-MSMS, neuroblastoma, ALK signaling,human

Jesper V. Olsen
contact affiliation	Novo Nordisk Foundation Center for Protein Research, Faculty of Health & Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
contact email	jesper.olsen@cpr.ku.dk
lab head
Kristina Bennet Emdal
contact affiliation	NNF Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen.
contact email	kristina.emdal@cpr.ku.dk
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/2018/11/PXD009477

PRIDE project URI

• PRIDE
  1. PXD009477
     1. Label: PRIDE project
     2. Name: Phosphoroteomics analysis of ALK signaling in neuroblastoma cells