msPurity

DOI: 10.18129/B9.bioc.msPurity  

Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Bioconductor version: Release (3.16)

msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.

Author: Thomas N. Lawson [aut, cre] , Ralf Weber [ctb], Martin Jones [ctb], Julien Saint-Vanne [ctb], Andris Jankevics [ctb], Mark Viant [ths], Warwick Dunn [ths]

Maintainer: Thomas N. Lawson <thomas.nigel.lawson at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("msPurity")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("msPurity")

 

HTML	R Script	msPurity
HTML	R Script	msPurity spectral database schema
HTML	R Script	msPurity spectral matching
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	MassSpectrometry, Metabolomics, Software
Version	1.24.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	GPL-3 + file LICENSE
Depends	Rcpp
Imports	plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite
LinkingTo
Suggests	MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL
SystemRequirements
Enhances
URL	https://github.com/computational-metabolomics/msPurity/
BugReports	https://github.com/computational-metabolomics/msPurity/issues/new
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	msPurity_1.24.0.tar.gz
Windows Binary	msPurity_1.24.0.zip
macOS Binary (x86_64)	msPurity_1.24.0.tgz
macOS Binary (arm64)	msPurity_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/msPurity
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/msPurity
Bioc Package Browser	https://code.bioconductor.org/browse/msPurity/
Package Short Url	https://bioconductor.org/packages/msPurity/
Package Downloads Report	Download Stats