PXD044306

PXD044306 is an original dataset announced via ProteomeXchange.

Title	Deep serum proteomics detects sex-influenced signature in a murine model of Alzheimer's disease
Description	Alzheimer’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.
HostingRepository	PRIDE
AnnounceDate	2024-05-21
AnnouncementXML	Submission_2024-05-21_13:09:00.902.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kaushik Kumar Dey
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-02 13:56:52	ID requested
⏵ 1	2024-05-21 13:09:01	announced

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]

submitter keyword: proteomics,Alzheimer’s disease, mass spectrometry, plasma, serum, proteome, tandem mass tag, biomarker

Junmin Peng
contact affiliation	Professor 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 email	junmin.peng@stjude.org
lab head
Kaushik Kumar Dey
contact affiliation	Department of Structural Biology St. Jude Children’s Research Hospital 262 Danny Thomas Place Memphis 38105
contact email	kaushik.dey@stjude.org
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/2024/05/PXD044306

PRIDE project URI

• PRIDE
  1. PXD044306
     1. Label: PRIDE project
     2. Name: Deep serum proteomics detects sex-influenced signature in a murine model of Alzheimer's disease