Multi-region proteomics maps mitochondrial and proteostatic networks recovery by subthreshold magnetic stimulation in Alzheimer mice
Description
This dataset accompanies the manuscript "Multi-region proteomics maps mitochondrial and proteostatic networks recovery by subthreshold magnetic stimulation in Alzheimer mice." The study uses quantitative proteomics across multiple brain regions to map mitochondrial and proteostatic network changes in a mouse model of Alzheimer's disease, and to characterise their recovery following subthreshold magnetic stimulation. This Mendeley Data record contains the processed proteomics outputs and supporting materials for the manuscript: protein and peptide quantification matrices, search parameter files, sample metadata describing the experimental design (brain region, genotype, and treatment group), and analysis outputs supporting the figures and statistics in the manuscript. Raw spectra were searched with SequestHT (Proteome Discoverer) against the UniProt Mus musculus database (SwissProt + TrEMBL with isoforms, TaxID 10090, version 2024-01-24). Tryptic digestion was used with up to 2 missed cleavages and a minimum peptide length of 6 amino acids. Precursor mass tolerance was set to 10 ppm and fragment mass tolerance to 0.02 Da. Carbamidomethylation of cysteine was set as a static modification; oxidation of methionine and N-terminal acetylation were set as dynamic modifications. Peptide-spectrum matches were validated with Percolator using a concatenated target/decoy strategy with FDR thresholds of 1% (strict) and 5% (relaxed). Detailed search parameters are provided in the 02_search_parameters/ folder. The raw mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository under the dataset identifier PXD077354. This Mendeley Data record should be cited together with the PRIDE deposit and the associated manuscript.
Files
Steps to reproduce
1. Sample preparation and LC-MS/MS acquisition Brain tissue was dissected from the relevant regions of wild-type and 5xFAD mice (with and without subthreshold magnetic stimulation), lysed, and processed for bottom-up proteomics. Tryptic peptides were analysed by LC-MS/MS. Full sample preparation and instrument settings are described in the Methods section of the associated manuscript. 2. Database search Raw spectra (deposited at PRIDE: PXD077354) were searched with SequestHT in Proteome Discoverer against the UniProt Mus musculus database (SwissProt + TrEMBL with isoforms, TaxID 10090, version 2024-01-24). Settings: trypsin digestion (full), maximum 2 missed cleavages, minimum peptide length 6, precursor tolerance 10 ppm, fragment tolerance 0.02 Da, carbamidomethyl (C) as static modification, oxidation (M) and N-terminal acetylation as dynamic modifications. Full parameters are provided in 02_search_parameters/Search parameters.docx. 3. PSM validation Peptide-spectrum matches were validated with Percolator using a concatenated target/decoy strategy at 1% strict FDR and 5% relaxed FDR. 4. Processed outputs Protein- and peptide-level quantification matrices and downstream statistics (provided in 01_processed_data/) were generated from the validated PSMs and used to support the figures and conclusions of the manuscript. 5. Reproducing the analysis Full reproduction requires (a) the raw .raw files from PRIDE PXD077354, (b) the search parameters in this record, and (c) the database version specified above. Downstream statistical analysis can be reproduced from the processed matrices in this record using standard proteomics workflows.
Institutions
- Gwangju Institute of Science and TechnologyGwangju, Gwangju