DEPstoi: DEPstoi: A package for stoichiometry analysis of label-free...

In arnesmits/DEPstoi: Stoichiometry analysis of label-free proteomics data

Description

This package provides the analysis workflow for stoichiometry analysis of data from affinity purification experiments followed by mass spectrometry analysis (AP-MS) as published previously ( ref). The package is an extention of the DEP package and it requires tabular input as generated by MaxQuant with iBAQ quantification enabled. Functions are provided for the analysis and visualization. For scientists with limited experience in R, the package also contains wrapper functions that entail the complete analysis workflow and generate a report.

Shiny apps

• run_app: Shiny apps for interactive analysis.

Workflow functions

• iBAQ: iBAQ-based stoichiometry workflow wrapper.

Functions

• merge_ibaq: Merge iBAQ intensities of protein groups with shared peptides.

• get_stoichiometry: Calculate relative stoichiometry of all significant proteins.

• plot_stoichiometry: Barplot of relative stoichiometries.

• plot_ibaq: Scatter plot of fold changes versus iBAQ intensity.

Example data

• GFPip: EED protein interactors (IP-MS dataset) (Kloet et al. Nat. Struct. Mol. Biol. 2016).

• GFPip_ExpDesign: Experimental design of the GFPip dataset.

• GFPip_pep: Peptides table of the GFPip dataset.

arnesmits/DEPstoi documentation built on May 3, 2019, 4:31 p.m.