/mehta2020-pi-proteome

Scripts and datasets used in Mehta et al., (2020) Phosphate and phosphite differentially impact the proteome and phosphoproteome of phosphate-deprived Arabidopsis suspension cell cultures

Primary LanguageHTMLGNU Affero General Public License v3.0AGPL-3.0

Phosphoproteomics and proteomics of Arabdidopsis cells re-fed phosphate and phosphite.

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

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.

R Plotting Scripts

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.