PXD018658

PXD018658 is an original dataset announced via ProteomeXchange.

Title	Ultra Deep Mouse cerebrospinal fluid (CSF) profiling in Alzheimer’s disease
Description	Alzheimer's disease (AD) is a neurodegenerative disease, the most common cause of dementia in elderly persons. Accumulation of amyloid plaques in the brain is a characteristic of AD. The requirements for a biomarker include the ability to measure a pathologic process, predict outcome, distinguish disease or measure a pharmacological response to a drug treatment or therapeutic intervention. However, there are no reliable blood based biomarkers for AD. CSF-based protein measurement can be used as a practice for biomarkers in human disease, but comprehensive profiling of Mouse CSF proteome is often masked by the twenty most abundant proteins and impacted by large dynamic range. The commonly used depletion method can alleviate the challenge but introduce additional experimental variation. Here we present a deep analysis of un-depleted CSF proteome by combining 11-plex TMT labeling, exhaustive 2D liquid chromatography fractionation, and high resolution tandem mass spectrometry. This platform is capable of identifying 1056 protein components, covering 6 orders of dynamic range, representing one of the proteome datasets. Finally, a subset of proteins, show statistically significant difference between AD and control samples, which may serve as biomarker candidates for the AD when further correlation can be drawn from the human proteome.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_00:24:30.554.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kaushik Dey
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-19 09:51:19	ID requested
⏵ 1	2021-09-09 00:24:31	announced

Wang H, Dey KK, Chen PC, Li Y, Niu M, Cho JH, Wang X, Bai B, Jiao Y, Chepyala SR, Haroutunian V, Zhang B, Beach TG, Peng J, Integrated analysis of ultra-deep proteomes in cortex, cerebrospinal fluid and serum reveals a mitochondrial signature in Alzheimer's disease. Mol Neurodegener, 15(1):43(2020) [pubmed]

submitter keyword: Alzheimer’s disease, biomarker, Mouse, CSF, mass spectrometry, proteomics, proteome, tandem mass tag

Junmin Peng
contact affiliation	Junmin Peng, PhD, Member (Professor) Structural Biology & Developmental Neurobiology Director, Center for Proteomics and Metabolomics St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis, TN 38105-3678
contact email	Junmin.peng@STJUDE.ORG
lab head
Kaushik Dey
contact affiliation	Postdoctoral Research Associate Department  Of  Structural Biology Mail Stop 311, Lab No: D1046 St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis, TN 38105-3678
contact email	kaushik1011@gmail.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/2021/09/PXD018658

PRIDE project URI

• PRIDE
  1. PXD018658
     1. Label: PRIDE project
     2. Name: Ultra Deep Mouse cerebrospinal fluid (CSF) profiling in Alzheimer’s disease