pRoteomics

pRoteomics is the publication-facing spatial proteomics workflow for hippocampal neuronal neuropil, neuronal soma, and microglia/PVM-enriched ROI datasets.

pipeline.yml is the only active machine-readable source of truth for script order, dataset support, inputs, outputs, and safe-rerun status. Start with WORKFLOW.md for the plain-language scientific workflow, then use RUN_ORDER.md as the detailed command reference.

Quick Start

Rscript run_dataset_pipeline.R --list-stages
Rscript run_dataset_pipeline.R --dataset microglia --stage modules_downstream --dry-run
Rscript run_dataset_pipeline.R --dataset all --stage integration --dry-run

Run named stages from pipeline.yml after private inputs are available:

Rscript run_dataset_pipeline.R --dataset <dataset> --stage core
Rscript run_dataset_pipeline.R --dataset <dataset> --stage qc
Rscript run_dataset_pipeline.R --dataset <dataset> --stage enrichment
Rscript run_dataset_pipeline.R --dataset <dataset> --stage modules_wgcna
Rscript run_dataset_pipeline.R --dataset <dataset> --stage modules_downstream
Rscript run_dataset_pipeline.R --dataset all --stage integration

Valid dataset families are neuron_neuropil, neuron_soma, and microglia. Microglia data are region-only microglia/PVM-enriched ROI/local microenvironment proteomics, not purified microglia.

The authoritative control compartment-marker validation is 03_qc_exploration/04e_control_compartment_abundance_publication_figures.r. It uses reconstructed observed, non-imputed abundance and animal-level descriptive summaries; it does not estimate purity, cell fractions, deconvolution, copy number, or total hippocampal abundance.

Repository Map

pipeline.yml                         active pipeline registry
WORKFLOW.md                          plain-language workflow guide
RUN_ORDER.md                         detailed command reference
run_dataset_pipeline.R               registry-driven launcher
docs/                                reviewer and maintenance documentation
R/                                   shared path, registry, validation, and dataset helpers
figures/                             explicit Figure 2/3 entry points and panel contract
01_preprocessing/                    preprocessing handoff
02_id_mapping/                       protein/gene identifier mapping
03_qc_exploration/                   QC, marker, and confounding checks
04_differential_expression_enrichment/ differential abundance and enrichment analyses
05_celltype_enrichment_EWCE/         EWCE analyses
06_modules_WGCNA/                    WGCNA construction and downstream module interpretation
07_spatial_networks/                 spatial network analyses
08_behavior_physio_coupling/         behavior/physiology coupling
10_biological_integration/           manuscript-level evidence synthesis
09_export_pride_journal/             active PRIDE, manuscript, and source-data export module
09_pride_submission/                 legacy helper code only
pride_submission/                    generated, gitignored local deposition payload
tests/                               private-data-independent tests

The folder name 04_differential_expression_enrichment/ is retained for compatibility, but manuscript-facing text should describe these outputs as differential abundance and enrichment results.

Documentation

• Workflow
• Command reference
• Documentation map
• WGCNA workflow
• Datasets
• Input contracts
• Output contracts
• Microglia ROI interpretation
• Reviewer reproducibility
• PRIDE export

Active vs Legacy

Active scripts are listed only in pipeline.yml. Legacy filenames are tracked in the legacy section of pipeline.yml and documented in docs/NAMING_MIGRATION.md.

09_export_pride_journal/ is the active export module. 09_pride_submission/ is retained as legacy helper code and should not be used as the active PRIDE workflow.

Reproducibility

CI and reviewer dry-runs validate the registry, script availability, dataset capabilities, and table contracts without private raw data. Full scientific runs require the private source matrices, metadata, raw/vendor files, and local deposition payload described in the manuscript data availability statement.

Author

Tobias Pohl