PXD041045

PXD041045 is an original dataset announced via ProteomeXchange.

Title	Suspension TRAPping filter (sTRAP) sample preparation for quantitative proteomics in the low µg input range using a plasmid DNA micro-spin column: analysis of the hippocampus from the 5xFAD Alzheimer’s Disease mouse model
Description	Suspension TRAPping filter (sTRAP) is an attractive sample preparation method for proteomics study. Here, we demonstrated the use of a low-cost Plasmid DNA spin column for sTRAP. We first evaluated, the reproducibility of this protocol and the low CoV using 4 replicates of 5-10 µg of a synapse enriched fraction, with 120 ng of the resulting tryptic peptides for mass spectrometry resulted in 5500 protein groups identification with CoV of 3.5%. We have also tested lower input amounts of 0.6 µg and 0.3 µg with CoV increase slightly to 5-8%. Comparing other sample preparation protocols, as the in-gel digestion and the commercial protifi sTRAP with the plasmid DNA micro-spin, the last is superior in both protein and peptide identification numbers (48523, 56714 to 60245 peptides and 5669, 6106, 6494 proteins respectively) and smaller Coefficient of Variation ( 6.7%, 3.2%, 3.1% respectively).We applied this protocol to the analysis of hippocampal proteome from a mouse model of Alzheimer’s disease, and identified about 6300 protein groups with CV of 11.6-14.6%. Protein changes in the mutant mice points to the alteration of processes related to known major AD-related pathology.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:00:30.821.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Evangelia Thanou
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	methylthiolated residue; monohydroxylated residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-23 04:13:38	ID requested
1	2023-05-23 11:28:39	announced
⏵ 2	2023-11-14 09:00:31	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Alzheimer’s disease, proteomics, 5xFAD mouse model, micro-spin column,sTRAP

Ka Wan Li
contact affiliation	Center for Neurogenomics and Cognitive Research, Department of Molecular and Cellular Neurobiology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
contact email	e.thanou@vu.nl
lab head
Evangelia Thanou
contact affiliation	Center for Neurogenomics and Cognitive Research, Department of Molecular and Cellular Neurobiology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
contact email	e.thanou@vu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD041045
     1. Label: PRIDE project
     2. Name: Suspension TRAPping filter (sTRAP) sample preparation for quantitative proteomics in the low µg input range using a plasmid DNA micro-spin column: analysis of the hippocampus from the 5xFAD Alzheimer’s Disease mouse model