PXD068000-1

PXD068000 is an original dataset announced via ProteomeXchange.

Title	Proteomics of Duchenne Muscular Dystrophy Patient iPSC - Derived Skeletal Muscle Cells Reveal Differential Expression of Myosin 9, Collagen 18A, Tropomyosin 1, NCAM1, BASP1 and RUVBL1
Description	Proteomics of skeletal muscular dystrophies is limited by the amount of protein which can be provided from patient biopsies. Cells and tissues derived from patient induced pluripotent stem cells (iPSCs) can be an expandable alternative source. We have patterned iPSCs from three Du-chenne Muscular Dystrophy (DMD) patient lines into skeletal muscle cells using a 2-dimensional as well as our 3-dimensional organoid differentiation system. Probes with sufficient protein amounts could be extracted and prepared for mass spectrometry. In total, 3007 proteins in 2D and 2709 proteins in 3D were detected in DMD patient probes. 83 proteins in 2D and 338 proteins in 3D can be described as differentially expressed between DMD and control patient probes in a post-hoc-Test. We have identified and propose Myosin-9, Collagen 18A, Tropomyosin 1, BASP1, RUVBL1 and NCAM1 as proteins specifically altered in their expression in DMD for further in-vestigations. Proteomics of skeletal muscle organoids resulted in greater consistency of results between cell lines in comparison to the 2-dimensional myogenic differentiation protocol.
HostingRepository	PRIDE
AnnounceDate	2025-11-17
AnnouncementXML	Submission_2025-11-16_17:23:25.927.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Britta Eggers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-02 09:42:33	ID requested
⏵ 1	2025-11-16 17:23:27	announced

Gallert SM, F, ö, lsch M, Mavrommatis L, Kindler U, Schork K, Eisenacher M, Vorgerd M, Brand-Saberi B, Eggers B, Marcus K, Zaehres H, Proteomics of Duchenne Muscular Dystrophy Patient iPSC-Derived Skeletal Muscle Cells Reveal Differential Expression of Cytoskeletal and Extracellular Matrix Proteins. Cells, 14(21):(2025) [pubmed]

10.3390/cells14211688;

submitter keyword: Organoids, Patient Induced Pluripotent Stem Cells, Disease Modelling,Duchenne Muscular Dystrophy, Proteomics, Skeletal Muscle

Katrin Marcus
contact affiliation	Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; 44801 Bochum, Germany
contact email	katrin.marcus@rub.de
lab head
Britta Eggers
contact affiliation	Ruhr University Bochum
contact email	britta.eggers@rub.de
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/2025/11/PXD068000

PRIDE project URI

• PRIDE
  1. PXD068000
     1. Label: PRIDE project
     2. Name: Proteomics of Duchenne Muscular Dystrophy Patient iPSC - Derived Skeletal Muscle Cells Reveal Differential Expression of Myosin 9, Collagen 18A, Tropomyosin 1, NCAM1, BASP1 and RUVBL1