PTM-compass

PTM-compass is a toolset for adapting and analyzing search engine results from multiple proteomics tools such as Comet-PTM, ReCom, and MSFragger. It standardizes output files, allowing them to be processed in downstream analysis workflows.

Installation

To install PTM-compass, clone this repository and ensure you have Python installed:

git clone https://github.com/CNIC-Proteomics/PTM-compass.git
cd PTM-compass

Setting Up a Virtual Environment

It’s recommended to create a virtual environment to manage dependencies for SHIFTS.

1. Create a virtual environment:

   python -m venv env

2. Activate the virtual environment:

   • On Windows:

     .\env\Scripts\activate

   • On macOS and Linux:

     source env/bin/activate

3. Install required dependencies:

   pip install -r python_requirements.txt

Requirements

The PTM-compass programs require Python 3.6 or above. All other dependencies are listed in the python_requirements.txt file.

Modules

Each PTM-Compass module is designed with specific functionality and configurable parameters. Modules primarily use a configuration file in INI format but also support overriding parameters via the command line.

For comprehensive instructions on using each module, please refer to the Module Guide.

Example Commands

For additional examples and tests, please consult the Test Guide.

License

This application is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) License. See the LICENSE file for details.