GEM_synergy

Overview

This repository contains code to analyze and plot the data from S. Hoefer et al. 2024. The required input files can be downloaded from Zenodo (10.5281/zenodo.10792252). More information on required input files and details on data processing steps are provided in the code.

SIMSI-Transfer Input and Output

The MaxQuant results needed as input to SIMSI-Transfer (kusterlab/SIMSI-Transfer), and the SIMSI-Transfer output tables can be downloaded from PRIDE (PXD050707).

Annotation of Phosphorylation Sites

Before starting data processing of decryptM experiments for CurveCurator (kusterlab/curve_curator), phosphorylation site annotations were added to the SIMSI-Transfer output (p10_evidence.txt). To reproduce this, inside python_environment, run the following commands:

conda env create -f gemsynergy_env.yaml -n gemsynergy
conda activate gemsynergy
python gemsynergy_pSiteAnnotation.py

The required files gemsynergy_env.yaml and gemsynergy_pSiteAnnotation.py are provided in this repository. The file Phosphosite_seq.fasta can be downloaded from PRIDE (PXD050707).