PXD021633

PXD021633 is an original dataset announced via ProteomeXchange.

Title	Comparative proteomic analysis in adult parrot and chicken plasma and cerebrospinal fluid identifies gene products involved in neurogenesis, neural cell differentiation and synaptic plasticity.
Description	Cerebrospinal fluid (CSF) proteins regulate neurogenesis, homeostasis and participate in active signalling during neuroinflammation. Components of CSF are mostly blood-derived, but partially also secreted from the brain cells. While various birds may represent suitable models for the investigation of adult constitutive neurogenesis, proteomic studies of the avian CSF examined so far solely chicken embryos. On this basis, we explored the proteomic composition of CSF and plasma in adult parrots, budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus) and chickens (Gallus gallus) using liquid chromatography–tandem mass spectrometry (nLC-MS/MS). To overcome the lack of a complete cockatiel genome information, we compared the MS/MS identification success rates after mapping all spectra from all three species against the reference proteomes of three model avian species: chicken, budgerigar and zebra finch. We show highest efficiency (8.8-4.7%) for the closest reference proteome, although part of the proteins (7.2-18%) were mapped only with other references. After filtering the selected datasets, we identified up to 746 proteins represented in the CSF and plasma of chicken, budgerigar and cockatiel. Enrichment analysis of the core proteome of these datasets revealed various metabolic and signalling pathways. Comparative analysis of CSF and plasma for each species then indicated clusters of proteins preferentially upregulated into CSF that were involved in neurogenesis, neural development and neural differentiation pathways. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel molecular evidence supporting the adult neurogenesis in birds.
HostingRepository	PRIDE
AnnounceDate	2021-05-18
AnnouncementXML	Submission_2021-05-18_08:42:23.547.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karel Harant
SpeciesList	scientific name: Nymphicus hollandicus; NCBI TaxID: 13180; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Melopsittacus undulatus; NCBI TaxID: 13146;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-22 09:07:12	ID requested
⏵ 1	2021-05-18 08:42:25	announced

Voukali E, Veetil NK, N, ě, mec P, Stopka P, Vinkler M, Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds. Sci Rep, 11(1):5312(2021) [pubmed]

submitter keyword: Melopsittacus undulatus, Nymphicus hollandicus, Gallus gallus

Michal Vinkler
contact affiliation	Division of Animal Evolutionary Biology, Department of Zoology Faculty of Science, Charles University in Prague Viničná 7, 128 44 Praha, Czech Republic
contact email	michal.vinkler@natur.cuni.cz
lab head
Karel Harant
contact affiliation	Charles University
contact email	harant@natur.cuni.cz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021633
     1. Label: PRIDE project
     2. Name: Comparative proteomic analysis in adult parrot and chicken plasma and cerebrospinal fluid identifies gene products involved in neurogenesis, neural cell differentiation and synaptic plasticity.