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README
Author: Gustaw Eriksson
Date: 2023-06-30
Version: 1.0
Contact: gustaw.eriksson@ki.se

Introduction

This proteomics analysis pipeline is based on the 'DEP: Differential Enrichment analysis of Proteomics data' package by Arne Smits and used for E Stener Victorin et al. (2023) eLife. It was implemented to investigate differentially expressed proteins and phosphorylation sites from tandem mass spectrometry of adipose tissue and skeletal muscle from women with and without polycystic ovary syndrome (PCOS) and in PCOS women after 5 weeks of treatment with electrical stimulation of the tissues.

Tutorial

Download FAT-MUS-Proteomics_workflow.R and the bin directory and to your project directory including the data folder. Please read the script and change the variables to match your specific needs. Data used for E Stener Victorin et al. (2023) eLife is available at request by contacting gustaw.eriksson@ki.se or anna.benrick@gu.se.

FAT-MUS-Proteomics_workflow.R will generate the output directory and output generated figures and tables to its designated output folders.