Scripts and datasets used in Mehta D, Ghahremani M, Pérez-Fernández M, Tan M, Schläpfer P, Plaxton WC and Uhrig RG. (2020) Phosphate and phosphite differentially impact the proteome and phosphoproteome of Arabidopsis suspension cell cultures
PSMFinder.py
is a script that takes a list of phosphopeptides generated from Perseus and MaxQuant as input, maps them against a proteome file and outputs a list of peptide sequences of a defined length centered at the phosphorylated site. It then reformats this output for motif enrichment analysis using the MoMo toot from Meme suite.
For details on usage, refer to the Readme file in /PSMFinder
.
Scripts used to produce various graphs used in the manuscript. Data files used are provided. To reproduce, edit input file locations in the R scripts.