DOI: 10.18129/B9.bioc.msPurity    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see msPurity.

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

Bioconductor version: 3.11

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, Ralf Weber, Martin Jones, Mark Viant, Warwick Dunn

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

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


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


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


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



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


biocViews MassSpectrometry, Metabolomics, Software
Version 1.14.1
In Bioconductor since BioC 3.4 (R-3.3) (4 years)
License GPL (>= 2)
Depends Rcpp
Imports plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite, uuid, jsonlite
Suggests testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL
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_1.14.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra) msPurity_1.14.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: