PXD022649

PXD022649 is an original dataset announced via ProteomeXchange.

Title	The power of many: Combining published datasets to identify Alzheimer’s disease biomarkers in cerebrospinal fluid
Description	This manuscript describes methodology for the meta-analysis of published proteomics datasets from multiple publications to mine for cerebrospinal fluid (CSF)-based diagnostic biomarkers for Alzheimer’s disease (AD).The identified biomarkers are then validated in an independent cohort analyzed in house and two additional published large datasets. Specifically, the published data was mined from 6 independent and a 7th in-house acquired CSF proteomic datasets resulting in a meta-cohort with 73 AD cases and 77 controls. In-depth data analysis revealed 35 CSF biomarker candidates, many of which are associated with brain glucose homeostasis, which is described to be dysregulated in AD. Next, the list of identified biomarker candidates were then validated in a 2-pronged approach using i) an independent cohort analyzed in house, and ii) two recently published independent large scale datasets comprising in total more than 500 samples. The resulting biomarker panel consisting of three glycolytic enzymes was found to discriminate AD from controls. To our knowledge, this is the first study that described the mining and systematic re-analysis of previously published liquid chromatography mass spectrometry-based proteomics data to identify and validate biomarkers in general and CSF biomarkers for AD in particular. While the presented study focused on AD, the presented workflow can be applied to any disease for which published datasets are available.
HostingRepository	PRIDE
AnnounceDate	2023-02-16
AnnouncementXML	Submission_2023-02-16_02:57:55.412.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Patrickvan Zalm
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized amino-terminal residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-20 07:00:30	ID requested
⏵ 1	2023-02-16 02:57:55	announced

Dataset with its publication pending

submitter keyword: Human, meta-analysis, Cerebrospinal Fluid, shotgun proteomics, LC-MS, Alzheimer's Disease, biomarker

Dr. HannoSteen
contact affiliation	Boston Childrens Hospital Steen Lab Department of Pathology Boston, MA, USA
contact email	hanno.steen@childrens.harvard.edu
lab head
Patrickvan Zalm
contact affiliation	Boston Children's Hospital Harvard Medical School Maastricht University
contact email	patrick.vanzalm@childrens.harvard.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/2023/02/PXD022649

PRIDE project URI

• PRIDE
  1. PXD022649
     1. Label: PRIDE project
     2. Name: The power of many: Combining published datasets to identify Alzheimer’s disease biomarkers in cerebrospinal fluid