⮝ Full datasets listing

PXD044306

PXD044306 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDeep serum proteomics detects sex-influenced signature in a murine model of Alzheimer's disease
DescriptionAlzheimer’s disease (AD) is the most common neurodegenerative disorder and is categorized by the deposition of extracellular amyloid plaques and intracellular neurofibrillary tangles. By using mouse models and performing In-depth analysis of the serum proteome has the potential to identify biomarkers that would allow for both early disease detection and measurement of disease progression. Here, we present an ultra-deep, multiplexed, undepleted mouse serum proteome by combining TMT pro-16-plex tandem-mass-tag (TMT)-based labeling, exhaustive two-dimensional liquid chromatography (LC/LC) fractionation, and sample concatenation based on the peptide concentration intensity (low, medium, and high) coupled with high resolution tandem mass spectrometry (MS/MS). We optimized a platform capable of analyzing 4100 protein components (3788 genes), covering a dynamic range of at least 6 orders of magnitude, representing one of the deepest serum proteome analyses by extensive fractionation and concatenation to date. Differential expression (DE) analysis between WT and 5xFAD mouse models showed essentially no protein changes except Lcn11. Interesting, our method detected 65 sex-dependent DE proteins with statistical significance (FDR < 0.05), including some earlier reported molecules related towards AD disease progression Serpina3h, Serpina3c, A1bg, Ncam2, Fgl1, Hamp, Kif15, Man2b2, Egfr, Prl etc, had adequate sensitivity and reproducibility to detect sex-dependent differentially expressed proteins in disease-related pathways. Hence, our newly developed protocol revealed alterations in key sex-related proteins that can be differentiated in serum analysis, both known and novel, which may be relevant to the development of assays for the monitoring and/or treatment various diseases.
HostingRepositoryPRIDE
AnnounceDate2024-05-21
AnnouncementXMLSubmission_2024-05-21_13:09:00.902.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKaushik Kumar Dey
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListiodoacetamide derivatized residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-08-02 13:56:52ID requested
12024-05-21 13:09:01announced
Publication List
10.1021/acs.jproteome.3c00496;
Dey KK, Yarbro JM, Liu D, Han X, Wang Z, Jiao Y, Wu Z, Yang S, Lee D, Dasgupta A, Yuan ZF, Wang X, Zhu L, Peng J, Identifying Sex-Specific Serum Patterns of Alzheimer's Mice through Deep TMT Profiling and a Concentration-Dependent Concatenation Strategy. J Proteome Res, 22(12):3843-3853(2023) [pubmed]
Keyword List
submitter keyword: proteomics,Alzheimer’s disease, mass spectrometry, plasma, serum, proteome, tandem mass tag, biomarker
Contact List
Junmin Peng
contact affiliationProfessor Department of Structural Biology Department of Developmental Neurobiology MS 311, D1034C (office) & D1039, D1046 (lab) St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis, TN 38105-3678
contact emailjunmin.peng@stjude.org
lab head
Kaushik Kumar Dey
contact affiliationDepartment of Structural Biology St. Jude Children’s Research Hospital 262 Danny Thomas Place Memphis 38105
contact emailkaushik.dey@stjude.org
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/2024/05/PXD044306
PRIDE project URI
Repository Record List
[ + ]