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msPurity

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("msPurity")):

Installation

To install this package, start R (version "4.3") 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")
msPurity HTML R Script
msPurity spectral database schema HTML R Script
msPurity spectral matching HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews MassSpectrometry, Metabolomics, Software
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3 + file LICENSE
Depends Rcpp
Imports plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite
System Requirements
URL https://github.com/computational-metabolomics/msPurity/
Bug Reports https://github.com/computational-metabolomics/msPurity/issues/new
See More
Suggests MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL
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Package Archives

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

Source Package msPurity_1.28.0.tar.gz
Windows Binary msPurity_1.28.0.zip (64-bit only)
macOS Binary (x86_64) msPurity_1.28.0.tgz
macOS Binary (arm64) msPurity_1.28.0.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