shotgun-patchSCP

Patch-SCP: Linking Electrophysiology and Proteomics in Brain Slices

This repository contains the analysis code used in
"Patch-Clamp Single-Cell Proteomics in Acute Brain Slices: A Framework for Recording, Retrieval, and Interpretation" (Biorxiv DOI: https://doi.org/10.1101/2025.09.15.675920, 2025, under review).

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Contents

• Supplementary CSV/XLSX tables (Zip file)
• SynGO Analyses (Zip file)
• Example output plots (Zip file)
• R scripts for figure generation (Figures 2–6 and S2-3)

Figure (paper)	Script file name
Figure 2 – Protein overlap (Venn)	Figure 2 Venn Diagram.R
Figure 3B – Gigaseal preserved (BP Upset)	Figure 3B Gigaseal preserved upset for BPs.R
Figure 3C – Gigaseal preserved (BP Heatmap)	Figure 3C Gigaseal preserved BP Heatmap.R
Figure 5 – Split SynGO heatmaps	Figure 5 Split SynGO heatmap 9-23-25.R
Figure 6 – Ion channel heatmap (toggle for duplicates)	Figure 6 Channel Heatmap with toggle 9-26-25.R
Supplementary Figure S2A – BP Upset	S2A BP Upset 9-26-25.R
Supplementary Figure S2B – CC Upset	S2B CC Upset 9-26-25.R
Supplementary Figure S3 – GPCR heatmap (toggle)	S3 GPCR Heatmap with toggle 9-26-25.R

Data Availability

Raw and processed mass spectrometry data can be found using the MassIVE dataset identifier MSV000099156 and ProteomeXchange dataset identifier PXD068359. Supplementary tables S1–S3 are provided with the manuscript.

Usage

Note that all scripts require report.pg_matrix.tsv and SynGO analysis files. If raw spectra files and/or SynGO outputs are being analyzed differently, modify names in the metadata file. Then open R and run the scripts directly (e.g., source("Figure2_Venn_Diagram.R")). Scripts are annotated with input file paths and parameters. Script for Figure 5 must be run first.

Citation

If you use these scripts, please cite: Rodriguez et al., Biorxiv, 2025 (DOI: https://doi.org/10.1101/2025.09.15.675920).

Dependencies

All analyses were performed in R Version 4.3.3 with the following packages:

• readr
• readxl
• dplyr
• stringr
• tidyr
• lubridate
• ggplot2
• eulerr
• pheatmap
• ComplexHeatmap
• circlize
• RColorBrewer

To install all dependencies in one step:

install.packages(c("readr","readxl","dplyr","stringr","tidyr",
                   "lubridate","ggplot2","eulerr","pheatmap","RColorBrewer"))
BiocManager::install(c("ComplexHeatmap","circlize"))