PXD021886

PXD021886 is an original dataset announced via ProteomeXchange.

Title	Identification of dystrophin Dp71dΔ71 associated proteins in PC12 cells by quantitative proteomics
Description	Dystrophin Dp71 is the main product of the DMD (Duchenne muscular dystrophy) gene in the brain. Dystrophin Dp71 is essential for the development of the nervous system and its alteration is associated with intellectual disability. Different isoforms of Dp71, with different subcellular locations, are generated by alternative splicing; however, their functions have not been fully described. Here, we identified Dp71dΔ71-associated proteins to understand their functions. PC12 cells stably transfected with pTRE2pur-Myc/Dp71dΔ71 or the empty vector (EV, pTRE2pur-Myc) were analyzed by immunoprecipitation coupled with quantitative proteomics. Samples were resolved and digested in gel, and peptides were separated using a UHPLC ACQUITY M-Class. Spectral data were acquired in an MS with electrospray ionization and ion mobility separation Synapt G2-Si operated with data-independent acquisition and ion mobility spectrometry using the high-definition multiplexed MS/MS mode. We used the Hi3 method to quantify absolutely every protein detected. A total of 121 proteins were identified and absolutely quantified using the internal standard and the intensity of the most abundant peptides per protein with Progenesis QI software and the database UP000002494. Seven new proteins associated with Dp71dΔ71 were selected with at least 2-fold quantity between immunoprecipitated proteins of PC12 Myc/Dp71dΔ71 versus PC12 empty vector cells. Proteins included β-tubulin, S-adenosylmethionine synthase isoform type-2, adapter molecule crk, helicase with zinc finger 2, WD repeat domain 93, cyclin-L2 and myosin-10. Immunoprecipitation followed by quantitative proteomics revealed new proteins that interact with Dp71dΔ71. These proteins are related to cell migration or cell growth, suggesting that Dp71dΔ71 and its associated proteins are involved in these cell functions. The results lay the foundation for future research on the relationship between these proteins and dystrophin Dp71 isoforms
HostingRepository	PRIDE
AnnounceDate	2024-11-01
AnnouncementXML	Submission_2024-11-01_14:49:50.563.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emmanuel Rios-Castro
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	amidated residue; phosphorylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	SYNAPT G2-Si

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-08 00:35:56	ID requested
⏵ 1	2024-11-01 14:49:51	announced

10.1016/j.bbapap.2024.141049;

Azotla-Vilchis C, Merino-Jim, é, nez C, R, í, os-Castro E, Arag, ó, n J, Ceja V, Montanez C, -associated proteins in PC12 cells by quantitative proteomics. Biochim Biophys Acta Proteins Proteom, 1873(1):141049(2025) [pubmed]

submitter keyword: quantitative proteomics., Dp71, protein interaction,DMD

Silvia Cecilia Irene Montañez Ojeda
contact affiliation	Department of Genetics and Molecular Biology, Cinvestav-IPN
contact email	cecim@cinvestav.mx
lab head
Emmanuel Rios-Castro
contact affiliation	Cinvestav-IPN
contact email	eriosc@cinvestav.mx
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021886
     1. Label: PRIDE project
     2. Name: Identification of dystrophin Dp71dΔ71 associated proteins in PC12 cells by quantitative proteomics