Figure 1:  Experimental scheme for the collection of the proteomics data using data independent acquisition-mass spectrometry.

a) Brain tissue sections from 4 regions were analyzed for all groups.
b) Samples were prepared and analyzed in batches of 16, with 14 individual samples per batch selected by balanced randomization. Each batch contained an inter-brain region quality control sample generated from pooling portions of several individual samples from across all 4 brain regions sampled. Each batch also contained a brain region specific inter-batch quality control sample generated from pooling portions of individual samples within that brain region.
c) In addition to quality control samples, both protein and peptide sample processing controls were included in all samples to track system suitability.
d) For each batch an on-column data-independent acquisition chromatogram library is generated from overlapping, narrow window gas-phase fractionation of an inter-batch QC. Individual samples are acquired by a single injection wider window data-independent acquisition method. Peptide detection and scoring is performed using EncyclopeDIA, and extracted ion chromatograms integrated with Skyline.
e) The proteomics data is publicly available on the Panorama web server in 5 different states, each corresponding to the level of post-processing.

Level 0 represents the raw data in two different formats - the raw format is directly from the Thermo mass spectrometer and the mzML format is the demultiplexed version of the raw data (Proteowizard version 3.0.20064).

Level 1 describes the zipped Skyline document grouped by batch.

Level 2 is a csv file grouped by batch of the Skyline output with the integrated peak area for each peptide (row) in each replicate (column).

Level 3A is a csv file of the normalized peptide abundance across all batches.

Level 3B is a csv file of the normalized protein abundance across all batches.

Dashboard links to an interactive view of the data. Please note that not all brain regions have a dashboard.