PXD063192-1

PXD063192 is an original dataset announced via ProteomeXchange.

Title	Label-free LC-MS/MS analysis of proteins associated with expanded G4C2 hexanucleotide repeat-containing transcripts in human induced pluripotent stem cells
Description	Proteins co-localizing with RNA targets of interest in human induced pluripotent stem cells (iPSCs) were identified using our recently optimized hybridization-proximity labeling approach (HyPro2) combined with label-free mass spectrometry. Briefly, fixed and permeabilized iPSCs from an ALS patient (DN19V4) or a healthy donor (C0053) were hybridized with a digoxigenin-labeled antisense oligonucleotide probe targeting transcripts containing the G4C2 hexanucleotide repeat expansion, which is present in the C9orf72 gene in DN19V4 but not in C0053. Alternatively, a control probe set was used to target ACTB pre-mRNA, expressed in both DN19V4 and C0053. The purified HyPro2 enzyme, which contains a digoxigenin-binding domain and a modified ascorbate peroxidase domain, was then recruited to the RNA targets, enabling in vitro biotinylation of target-proximal proteins. Following streptavidin pull-down, biotinylated proteins were fragmented using a Trypsin/Lys-C protease mix and identified by label-free LC-MS/MS analysis. All experiments were performed in triplicate
HostingRepository	PRIDE
AnnounceDate	2025-08-12
AnnouncementXML	Submission_2025-08-12_03:23:18.052.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD063192
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Steven Lynham
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-22 06:17:33	ID requested
⏵ 1	2025-08-12 03:23:18	announced

10.6019/PXD063192;

submitter keyword: ACTB,RNA-protein interactions, C9orf72, pre-mRNA, hybridization-proximity labeling

Eugene Makeyev
contact affiliation	Centre for Developmental Neurobiology, King's College London
contact email	eugene.makeyev@kcl.ac.uk
lab head
Steven Lynham
contact affiliation	King's College London
contact email	steven.lynham@kcl.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063192
     1. Label: PRIDE project
     2. Name: Label-free LC-MS/MS analysis of proteins associated with expanded G4C2 hexanucleotide repeat-containing transcripts in human induced pluripotent stem cells