PXD044306 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-08-02 13:56:52 | ID requested | |
⏵ 1 | 2024-05-21 13:09:01 | announced | |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD044306
- Label: PRIDE project
- Name: Deep serum proteomics detects sex-influenced signature in a murine model of Alzheimer's disease