PXD025777

PXD025777 is an original dataset announced via ProteomeXchange.

Title	Age-dependent hippocampal proteomics in the APP/PS1 Alzheimer mouse model: a comparative analysis with classical SWATH/DIA and directDIA approaches
Description	Alzheimer’s disease (AD) is the most common neurodegenerative disorder in the human population, for which there is currently no cure. The cause of AD is unknown, however, the toxic effects of amyloid-β (Aβ) are believed to play a role in its onset. To investigate this, we examined changes in global protein levels in a hippocampal synaptosome fraction of the APP/PS1 mouse model of AD at 6 and 12 months of age (moa). Data independent acquisition (DIA), or SWATH, was used for a quantitative label-free proteomics analysis. We first assessed the usefulness of a recently improved directDIA workflow as alternative to conventional DIA data analysis using a project specific spectral library. Subsequently, we applied directDIA to the 6- and 12-moa APP/PS1 datasets and applied the Mass Spectrometry Downstream Analysis Pipeline (MS-DAP) for differential expression analysis and candidate discovery. We observed most regulation at 12-moa, in particular of proteins involved in Aβ homeostasis and microglial dependent synaptic pruning and/or immune response, such as APOE, CLU and C1QA-C
HostingRepository	PRIDE
AnnounceDate	2021-06-24
AnnouncementXML	Submission_2021-06-24_01:47:23.576.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sophie van der Spek
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	L-cysteine methyl disulfide
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-03 23:10:34	ID requested
⏵ 1	2021-06-24 01:47:23	announced

Dataset with its publication pending

submitter keyword: APP/PS1 mouse model, Alzheimer, microglia, proteomics, directDIA, MS-DAP

Ka Wan Li
contact affiliation	Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
contact email	k.w.li@vu.nl
lab head
Sophie van der Spek
contact affiliation	CNCR, VU amsterdam
contact email	s.j.f.vander.spek@vu.nl
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/2021/06/PXD025777

PRIDE project URI

• PRIDE
  1. PXD025777
     1. Label: PRIDE project
     2. Name: Age-dependent hippocampal proteomics in the APP/PS1 Alzheimer mouse model: a comparative analysis with classical SWATH/DIA and directDIA approaches