PXD011216

PXD011216 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Proteomics identifies potential biomarkers and implicates the granin family in Parkinson’s disease
Description	Parkinson’s disease (PD) is the second most common neurodegenerative disorder. Treatments are available to address PD motor symptoms, but not disease progression or cognitive decline. Demonstrating disease modification in clinical trials is still a substantial challenge because of the high disease heterogeneity and variability in progression as well as subjectivity in clinical scoring. To develop novel therapeutics for PD, there is an urgent need to identify biomarkers for patient stratification in clinical trials. In this study, we used cutting edge data-independent acquisition (DIA) mass spectrometry to identify PD-specific biomarkers in patient cerebrospinal fluid (CSF). To identify novel biomarkers with minimal false discovery, two independent cohorts were analyzed by DIA mass spectrometry. An initial discovery cohort of 53 PD and 72 control (CTRL) patient samples was analyzed, identifying 53 proteins with significant changes (nominal p-value ≤ 0.05) in PD relative to CTRL out of the 342 detectable proteins. A second cohort of 28 PD and 43 CTRL samples were analyzed as above and identified 41 proteins with significant changes in PD. Thirteen proteins showed significant changes in both cohorts, some of which are previously reported to be altered in PD (i.e., EPHA4 and SERPINC1). Three members of a specific protein family, which are cleaved into bioactive peptides, were amongst these 13 proteins . Further, peptide-level quantification of the detectable members of this protein family (7 total) revealed that specific regions of all 7 proteins are decreased in Parkinson’s disease samples. Together, these data may implicate altered processing, localization, and/or function of this entire protein family for the first time in PD.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:49:01.091.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pablo Sardi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-28 05:51:40	ID requested
1	2020-02-18 06:53:10	announced
⏵ 2	2024-10-22 04:49:05	announced	2024-10-22: Updated project metadata.

Publication List

Rotunno MS, Lane M, Zhang W, Wolf P, Oliva P, Viel C, Wills AM, Alcalay RN, Scherzer CR, Shihabuddin LS, Zhang K, Sardi SP, Cerebrospinal fluid proteomics implicates the granin family in Parkinson's disease. Sci Rep, 10(1):2479(2020) [pubmed]
Bhat SA, Ahmad SM, Ibeagha-Awemu EM, Mobashir M, Dar MA, Mumtaz PT, Shah RA, Dar TA, Shabir N, Bhat HF, Ganai NA, Comparative milk proteome analysis of Kashmiri and Jersey cattle identifies differential expression of key proteins involved in immune system regulation and milk quality. BMC Genomics, 21(1):161(2020) [pubmed]
10.1038/s41598-020-59414-4;
10.1186/s12864-020-6574-4;

Rotunno MS, Lane M, Zhang W, Wolf P, Oliva P, Viel C, Wills AM, Alcalay RN, Scherzer CR, Shihabuddin LS, Zhang K, Sardi SP, Cerebrospinal fluid proteomics implicates the granin family in Parkinson's disease. Sci Rep, 10(1):2479(2020) [pubmed]

Bhat SA, Ahmad SM, Ibeagha-Awemu EM, Mobashir M, Dar MA, Mumtaz PT, Shah RA, Dar TA, Shabir N, Bhat HF, Ganai NA, Comparative milk proteome analysis of Kashmiri and Jersey cattle identifies differential expression of key proteins involved in immune system regulation and milk quality. BMC Genomics, 21(1):161(2020) [pubmed]

10.1038/s41598-020-59414-4;

10.1186/s12864-020-6574-4;

Keyword List

curator keyword: Biomedical
submitter keyword: cerebrospinal fluid,Parkinson's, CSF, Proteomics, biomarkers

curator keyword: Biomedical

submitter keyword: cerebrospinal fluid,Parkinson's, CSF, Proteomics, biomarkers

Contact List

Sergio Pablo Sardi
contact affiliation	CNS Genetic Diseases Research, Neuroscience Therapeutic Area, Sanofi, Inc., Framingham, MA 01701
contact email	pablo.sardi@sanofi.com
lab head
Pablo Sardi
contact affiliation	Sanofi
contact email	pablo.sardi@sanofi.com
dataset submitter

Full Dataset Link List

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/2020/02/PXD011216
PRIDE project URI

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/2020/02/PXD011216

PRIDE project URI

Repository Record List

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