Brain microprotein atlas of human frontal cortex in Alzheimer's disease—supporting data and figures

Supporting data and figure libraries for the manuscript "A microprotein atlas of the human frontal cortex in Alzheimer's disease" (Miller et al., 2026).

This deposit accompanies the GitHub code repository at https://github.com/brendan-miller-salk/brain-microprotein-atlas and contains the bulky reference files, master annotation tables, and per-microprotein figure libraries that exceed GitHub's per-file size limits. Together with the GitHub repository, these files are sufficient to (1) reproduce every summary table and supplemental table in the manuscript and (2) run the interactive Streamlit dashboard locally with full mirror-plot, expression-profile, and smORF-cartoon viewers enabled.

Contents (5 tarballs):

figures_mirror_plots.tar.gz (~2.3 GB) — PROSIT 3-panel spectral mirror plots (sequence ladder + mirror spectrum + ppm-error lollipop) for every PSM assigned to a microprotein in our TMT-MS searches, stratified by composite Confidence tier (Strong, Moderate, Weak, Insufficient). Files named PEPTIDE_zCHARGE_SCAN.{png,pdf}. Used by the Streamlit dashboard to back per-peptide spectral evidence display.

figures_expression_profiles.tar.gz (~1.9 GB) — Per-pair main-ORF / smORF triptych figures (scatter with group-coloured fits + main-ORF violin + smORF violin) routed into coupled/ and non_coupled/ based on |Δr| > 0.1 between AD and control groups in ROSMAP DLPFC. Files named GENE_chrX_start-end.{png,pdf}.

figures_smorf_cartoons.tar.gz (~623 MB) — Per-locus smORF cartoons keyed by genomic coordinate (chrX_start-end.{png,pdf}).

large_reference_files.tar.gz (~1.2 GB) — (a) Ensembl_and_Unreviewed_Brain_Microproteins.gtf (889 MB): combined GENCODE-v43 + unreviewed brain microprotein GTF used for FeatureCounts. (b) RiboCode reference outputs (ribocode_results.{gtf,bed,txt} and ribocode_results_collapsed.{gtf,bed,txt}) covering all annotated translated ORFs.

large_data_tables.tar.gz (~300 MB) — Master microprotein annotation + evidence table (microprotein_master.csv), the archived first-submission snapshot, the combined gene-pathway analysis (combined_gpath_results.csv), and TSS-motif prevalence (tss_motif_prevalence.csv).

How to use: clone the GitHub repository, then run the download_zenodo_assets.sh script in the repo root to fetch and extract these tarballs into the correct local paths. See DATA_AVAILABILITY.md in the repository for details.

Raw upstream data (FASTQ, mzML, ROSMAP/MSBB clinical metadata, dbGaP-controlled Ribo-seq) are not included here — they are available through the AD Knowledge Portal (Synapse), dbGaP, and the cited primary publications. See the manuscript Methods and DATA_AVAILABILITY.md.