Please continue to add to P3 as you see more tools will be needed.
This project is intended to be a living document of proteomic data processing, so please feel free to file issues as need be. These issues can be either bugs or features. Please do NOT merge code without filing an issue first.
If there is an issue or typo, please create an issue. Then you can fix the issue in your own branch (or fork) and then create a pull request.