Processing LiP-MS and LiP-Quant Data for Dynaprot

Step-by-Step Guide

1. Prepare the YAML Configuration File Create a configuration file based on the provided params_template.yaml. This file should include:

• The path to the Spectronaut output file

• Associated metadata required for database integration

2. Run the Appropriate R Script from the Command Line For LiP/TrP Experiments:

Rscript LiPTrPpipeline.R path/to/your_params.yaml

For LiP-Quant Experiments with Dose-Response:

Rscript LiPQuantPipeline.R path/to/your_params.yaml

3. Upload to Dynaprot After successful processing, use the generated output folder to upload results to the Dynaprot database on the virtual machine (VM).