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multiDIA

Analysis and figures for the multiDIA manuscript: Spectronaut directDIA reports from three parallel digests (trypsin, Lys-C, Glu-C) of one human PD brain cohort.

Layout

data/         inputs; nothing here is produced by the code
derived/      tables built from data/ and read by the figures
analysis/     all code, and its tests
figures/      the paper's figures: panels, whole figures and PNGs
build.sh      rebuilds derived/ and figures/ from data/
index.md …    the website, https://multidia.slavovlab.net (GitHub Pages: _config.yml, CNAME, *.md)
path contents
data/search/*-60min-Phospho.parquet the Spectronaut reports, one per digest, searched with variable phospho. Not in the repository (too large for GitHub); place them here to rebuild.
data/uniprot_sprot_2024-01-01_HUMAN_ISOFORMS.fasta the search database (UniProt Swiss-Prot human with isoforms, 2024-01-01)
data/metadata.xlsx the brain bank's neuropathology sheet; ADRC # is the patient id and NPDX1 gives the condition
data/uniprot/features_P10636.tsv.gz UniProt features of tau (Fig. 3c), downloaded once by fig3bc_phospho_atlas.py
derived/counts/ per-sample counts (Fig. 1b–c)
derived/da_iso/ discriminating-region and junction coverage of every isoform (Fig. 2d)
derived/mods/ the phospho scan and its site table (Fig. 3)
derived/multiDIA.sdrf.tsv the SDRF-Proteomics sample table for the PRIDE submission, one row per raw file (prep_sdrf.py)

Code

Each file in analysis/ is named for what it produces:

prefix role files
fig…_ draws that figure's panels fig1a_workflow, fig1b_depth, fig1cd_coverage, fig2a_isoform_strip, fig2b_ed1_isoform_da (Fig. 2b and the Extended Data Fig. 1 volcano), fig2cd_isoform_coverage, fig3a_phospho_sites, fig3bc_phospho_atlas
prep_ builds derived/ and the reports prep_counts, prep_phospho, prep_sdrf, prep_parquet (Spectronaut TSV export to the parquet reports)
lib_ shared by the figures lib_report (reports, run names, metadata), lib_fasta, lib_palette, lib_svg, lib_compose (stacking panels)

audit.py checks figures/ and test_units.py is the unit tests.

Rebuild

With the environment from pyproject.toml (uv sync), from the repository root:

./build.sh                                  # derived/ and every figure, then the checks
.venv/bin/python analysis/test_units.py     # unit tests, no data needed
.venv/bin/python analysis/audit.py          # whole figures and PNGs current, type >= 10 pt at 6.5 in wide, one font