Silencing mitochondrial gene expression in living cells

Proteomics analysis scripts

This repository holds the Python code for MS data analysis in the Paper "Silencing mitochondrial gene expression in living cells" (https://doi.org/10.1126/science.adr3498).

Systems requirements

• Scripts are provided as Jupyter notebooks.
• Analysis was performed using modules from the autoprot project which need to be installed on your local computer
  • Autoprot integrates Python and R scripts for proteomics data analysis and therefore requires both languages to be installed
• Software dependencies for autoprot are detailed in the ''requirements.txt'' file in the autoprot repository
  • However, detailed information on all installed packages during execution including version numbers are provided in the respective notebooks (as ''environment.txt'' and ''R_environment.csv'' respectively)
• The scripts were tested with Python 3.9.9 and R 4.2.2. All specific software versions for Python and R are documented with the environment.txt and R_environment.txt files in the respective data analysis folders.

Installation guide

• Install autoprot on your local computer (see installation instructions on the autoprot repository).
  • All analyses in this repository were performed with autoprot and cannot be run without it.
• Installation time largely depends on the time required to compile the R packages.
  • With a fast internet connection, the installation on a standard desktop computer should take less than 30 minutes.
• No non-standard libraries or hardware are required to run the scripts

How to run

• The repository contains two subfolders ND2_CYTB and ZNF703_DUSP11_SMIM26 corresponding to the knockdown and FLAG-IP described in the paper, respectively.
  • Within each folder, you must provide the MaxQuant search results for the code to run.
• You can find the data for the knockdowns at https://www.ebi.ac.uk/pride/archive/projects/PXD061846 (use the MaxQ_txt_CYTB_ND2-KDs.zip folder). The resulting directory structure should be as follows

.
├── ND2_CYTB
├── maxquant
│   └── 2h_nonfrac
│       ├── experimentalDesignTemplate.txt
│       ├── mqpar.xml
│       └── txt

• Data for the FLAG-IP analysis can be found at https://www.ebi.ac.uk/pride/archive/projects/PXD061877 (use the MaxQ_txt_FLAG-IPs.zip folder).

.
├── ZNF703_DUSP11_SMIM26
└── txt

• Execute the ipynb files in each directory. Note: You should import autoprot as autoprot_dev to run the code as is or change the import to whatever import alias you use for autoprot.

How to get help

If something does not work as expected, please reach out to us via the GitHub issues function.