PXD022667

PXD022667 is an original dataset announced via ProteomeXchange.

Title	Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data
Description	This submission contains human protein interaction datasets of four proteins (BCL2, TDP-43, MDM2, PTEN) across three cancer cell lines (G401, T47D, A375) and one iPSC-derived neuronal cell line (glutamatergic patterned induced neuron, GPiN). The data were generated to demonstrate the utility of Genoppi (lagelab.org/genoppi), an open-source computational tool that enables integration of quantitative proteomic results with genetic data. Our analyses show a general pattern of both cell-type-independent and cell-type-specific interactions for the tested proteins. In particular, our results suggest that the neuron-specific interactions of BCL2 and TDP-43 are mediating their genetic involvement in amyotrophic lateral sclerosis.
HostingRepository	PRIDE
AnnounceDate	2021-05-18
AnnouncementXML	Submission_2021-05-17_22:13:57.352.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kasper Lage
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-23 08:04:31	ID requested
1	2021-02-10 11:55:05	announced
2	2021-05-17 22:11:34	announced	2021-05-18: Updated project metadata.
⏵ 3	2021-05-17 22:13:58	announced	2021-05-18: Updated project metadata.

Pintacuda G, Lassen FH, Hsu YH, Kim A, Mart, í, n JM, Malolepsza E, Lim JK, Fornelos N, Eggan KC, Lage K, Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data. Nat Commun, 12(1):2580(2021) [pubmed]

submitter keyword: neuron and cancer cells, PTEN, BCL2, label-free quantification, MDM2, protein-protein interactions,endogenous IP-MS, TDP-43

Kasper Lage
contact affiliation	Massachusetts General Hospital, USA
contact email	lage.kasper@mgh.harvard.edu
lab head
Kasper Lage
contact affiliation	Massachusetts General Hospital
contact email	klagelab@gmail.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/2021/02/PXD022667

PRIDE project URI

• PRIDE
  1. PXD022667
     1. Label: PRIDE project
     2. Name: Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data