PXD042200-2

PXD042200 is an original dataset announced via ProteomeXchange.

Title	Deep Proteome of the Developing Chick Midbrain
Description	The epithelial-to-mesenchymal transition (EMT) and migration of cranial neural crest cells are critical processes that occur in the early embryo that permit proper craniofacial patterning. Disruptions in these processes not only impair development but also lead to various diseases, underscoring the need for their detailed understanding at the molecular level. The chick embryo has served historically as an excellent model for human embryonic development. While chick cranial neural crest cell EMT and migration have been characterized at the transcript level, studies at the protein level—to allow direct measurement of the active players—have not been undertaken to date. In this study, we applied mass spectrometry (MS)-based proteomics to establish a deep proteomics profile of the midbrain region during early embryonic development. We developed a proteomics method combining optimal lysis conditions and offline fractionation with nanoflow liquid chromatography coupled to high-resolution MS to analyze the tissue from this region, which identified >5,900 proteins involved in key pathways related to neural crest cell EMT and migration such as signaling, proteolysis/extracellular matrix (ECM), and transcriptional regulation. This study offers valuable insight into important developmental processes occurring in the midbrain region and demonstrates the utility of proteomics for characterization of various tissues during chick embryogenesis.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:09:33.965.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Nemes
SpeciesList	scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-12 17:57:10	ID requested
1	2023-10-24 19:56:43	announced
⏵ 2	2023-11-14 09:09:34	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: midbrain, bottom-up proteomics,chick embryo, cranial neural crest, LC-MS/MS

Peter Nemes
contact affiliation	Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742
contact email	nemes@umd.edu
lab head
Peter Nemes
contact affiliation	University of Maryland, College Park
contact email	nemes@umd.edu
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/2023/10/PXD042200

PRIDE project URI

• PRIDE
  1. PXD042200
     1. Label: PRIDE project
     2. Name: Deep Proteome of the Developing Chick Midbrain