README.md

In nktvslv/oxiquant: MS1 quantitation of intact and oxidized peptides

oxiquant

Automated analysis of mass spectrometry data collected for hydroxyl radical footprinting experiment

Description

oxiquant is a pipeline for quantitative proteomics that executes MS-GF+ MS2 search engine for peptides identification, mzcharge to extract intensity signal from MS1 spectra and maps identified peptides and their possible oxidated variants to extracted ion current.

Installation

To run MS-GF+ Java runtime has to be installed.

R dependencies from CRAN and Bioconductor

# CRAN packages
install.packages(c("data.table","future","future.apply"))

# Bioconductor packages
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(c("mzID","mzR"))

On Windows install Rtools from CRAN to compile C++ code in mzcharge

Install mzcharge

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("https://github.com/nktvslv/mzcharge.git")

Install oxiquant

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("https://github.com/nktvslv/oxiquant.git")

oxiquant is bundled with MS-GF+ release 2020.03.14 that will be downloaded during first execution of the pipeline and installed in package directory.

nktvslv/oxiquant documentation built on June 10, 2021, 3:16 p.m.