This project provides the basic analysis and tools for carrying out end-to-end proteomic analysis for data generated at PNNL. This repository will serve as a resource upon which we can build additional tools in a reusable fashion.

Check out the CONTRIBUTING.md document. We welcome all additional tool and methods. Then you can create a pull request and merge your code in.

Click on the Use this template button above. This will allow you to create your own repository.

This pipeline links together a series of data and code repositories to ensure that any data is saved for future use. Furthermore we hope to be able to reproduce the analysis for future projects. A brief overview of each tool is described here.

This processing relies on a series of customized R scripts that are in the following directories:

• global: global proteomics analysis documentation is here
• phospo: phosphoproteomics analysis documentation is here Once this analysis is complete, the data should be stored on Synapse

Synapse is used for:

• data storage: data is backed up for free
• data processing: UUIDs and permission modifications allow for easy analysis
• data release: data can be moved to the PDC or shared

You will need to acquire a synapse username to access synapse, and become a certified user to add data, but after that you will be set with future projects.

There are typically a few steps we do for functional analysis. They are described in the functional analysis directory for now.