PXD009646

PXD009646 is an original dataset announced via ProteomeXchange.

Title	Deep Dive in the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification
Description	Cerebrospinal fluid (CSF) is a body fluid of choice for biomarker studies of brain disorders but remains relatively under-studied compared to other biological fluids such as plasma, partly due to the more invasive means of its sample collection. The present study establishes an in-depth CSF proteome through the analysis of a unique CSF sample from a pool of healthy donors. After immuno-affinity depletion, the CSF sample was fractionated using off-gel electrophoresis and analyzed with liquid chromatography tandem mass spectrometry (MS) using the latest generation of hybrid Orbitrap mass spectrometers. The shotgun proteomic analysis allowed the identification of 20689 peptides mapping on 3379 proteins. To the best of our knowledge, the obtained dataset constitutes the largest CSF proteome published so far. Among the CSF proteins identified, 34% correspond to genes defined as elevated in the brain by The Human Protein Atlas. The principal Alzheimer disease biomarkers (e.g., tau protein, amyloid-β, apolipoprotein E and neurogranin) were detected. Importantly, our dataset significantly contributes to the Chromosome-Centric Human Proteome Project (C-HPP), and 13 proteins considered as missing are proposed for validation in accordance with the HPP guidelines.
HostingRepository	PRIDE
AnnounceDate	2018-08-29
AnnouncementXML	Submission_2018-08-29_03:49:18.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD009646
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Charlotte Macron
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Ammonia-loss; Deamidated; TMT6plex; Dehydrated; Oxidation; Acetyl; Carbamidomethyl
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-02 03:34:44	ID requested
⏵ 1	2018-08-29 03:49:19	announced

Macron C, Lane L, N, ú, ñ, ez Galindo A, Dayon L, Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification. J Proteome Res, 17(12):4113-4126(2018) [pubmed]

curator keyword: Biological

submitter keyword: augurin

brain

cerebrospinal fluid

Human Proteome Project

mass spectrometry

proteomics

missing proteins

tandem mass tag

Loïc Dayon
contact affiliation	Proteomics Team Leader, Nestlé Institute of Health Sciences SA
contact email	Loic.Dayon@rd.nestle.com
lab head
Charlotte Macron
contact affiliation	NIHS
contact email	charlotte.macron@rd.nestle.com
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/2018/08/PXD009646

PRIDE project URI

• PRIDE
  1. PXD009646
     1. Label: PRIDE project
     2. Name: Deep Dive in the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification