PXD040613-2

PXD040613 is an original dataset announced via ProteomeXchange.

Title	S-palmitoylation during retinoic acid induced neuronal differentiation of SH-SY5Y neuroblastoma cells
Description	S-palmitoylation is the covalent attachment of palmitic acid to cysteine residues through a thioester bond. S-palmitoylation is highly abundant in neurons, where it plays a fundamental role in neuronal development. In addition, S-palmitoylation is associated with many neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and Huntington's disease. However, knowledge of S-palmitoylation in neurodevelopment is limited due to technological challenges in analysing this highly hydrophobic modification of proteins. Here, we use two orthogonal methods, acyl-biotin exchange and lipid metabolic labelling, to identify S-acylated proteins and sites in neuronal cells. We identified 650 S-palmitoylated proteins by both methods, including proteins that are well-known for their role in neuronal differentiation. Importantly, significant changes in the abundance of S-palmitoylated proteins were detected during neuronal differentiation. Overall, the combination of methods described here provides the advantage of cross-validation of the identified S-palmitoylated proteins and should be used further to study S-palmitoylation in the central nervous system to understand physiology and neurodegenerative diseases.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:11:32.575.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Samiksha Sardana
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	palmitoylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-06 04:16:35	ID requested
1	2023-10-24 13:34:33	announced
⏵ 2	2023-11-14 09:11:40	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:12:51	announced	2024-10-22: Updated project metadata.

Sardana S, Nederstigt AE, Baggelaar MP, -Palmitoylation during Retinoic Acid-Induced Neuronal Differentiation of SH-SY5Y Neuroblastoma Cells. J Proteome Res, 22(7):2421-2435(2023) [pubmed]

submitter keyword: acyl-biotin exchange, lipid metabolic labelling,Protein S-palmitoylation, SH-SY5Y differentiation, retinoic acid, mass spectrometry-based proteomics

Marc Pieter Baggelaar
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH The Netherlands Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
contact email	m.p.baggelaar@uu.nl
lab head
Samiksha Sardana
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
contact email	s.sardana@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040613
     1. Label: PRIDE project
     2. Name: S-palmitoylation during retinoic acid induced neuronal differentiation of SH-SY5Y neuroblastoma cells