Package: msPurity
Type: Package
Title: Automated Evaluation of Precursor Ion Purity for Mass
        Spectrometry Based Fragmentation in Metabolomics
Version: 1.38.0
Date: 2025-03-10
Authors@R: c(
    person(given = "Thomas N.", family = "Lawson",
        email = "thomas.nigel.lawson@gmail.com", role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-5915-7980")),
    person(given = "Ralf", family = "Weber", role = "ctb"),
    person(given = "Martin", family = "Jones", role = "ctb"),
    person(given = "Julien", family = "Saint-Vanne", role = "ctb"),
    person(given = "Andris", family = "Jankevics", role = "ctb"),
    person(given = "Ossama", family = "Edbali",
        email = "o.edbali@bham.ac.uk", role = "ctb",
        comment = c(ORCID = "0000-0003-0132-8668")),
    person(given = "Mark", family = "Viant", role = "ths"),
    person(given = "Warwick", family = "Dunn", role = "ths"))
URL: https://github.com/computational-metabolomics/msPurity/
Description: 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.
Encoding: UTF-8
License: GPL-3 + file LICENSE
BugReports: https://github.com/computational-metabolomics/msPurity/issues/new
Depends: Rcpp
Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
        stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite,
        BiocFileCache
Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown,
        msPurityData, CAMERA, RPostgres, RMySQL
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)
biocViews: MassSpectrometry, Metabolomics, Software
Collate: 'all-generics.R' 'averaging.R' 'combineAnnotations.R'
        'create-database.R' 'createDatabase.R' 'flag-filter-remove.R'
        'iw-norm.R' 'matching-algs.R' 'meta_extract.R' 'msPurity.R'
        'pcalc.R' 'purityA-0-class.R' 'purityA-av-spectra.R'
        'purityA-constructor.R' 'purityA-create-msp.R'
        'purityA-filter-frag-spectra.R' 'purityA-frag4feature.R'
        'purityA-validate.R' 'purityD-class.R' 'purityD-constructor.R'
        'purityD-av-spectra.R' 'purityD-dims-purity.R'
        'purityD-fileList.R' 'purityD-filterp.R' 'purityD-subtract.R'
        'purityD-writeOut.R' 'purityX-class.R' 'purityX-constructor.R'
        'spectral-matching.R' 'spectralMatching.R' 'splinepurity.R'
Config/pak/sysreqs: libicu-dev libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:43:35 UTC
RemoteUrl: https://github.com/bioc/msPurity
RemoteRef: RELEASE_3_23
RemoteSha: d6812680e805447a50753dd1b15b5a8d46629727
NeedsCompilation: no
Packaged: 2026-04-29 23:38:43 UTC; root
Author: Thomas N. Lawson [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5915-7980>),
  Ralf Weber [ctb],
  Martin Jones [ctb],
  Julien Saint-Vanne [ctb],
  Andris Jankevics [ctb],
  Ossama Edbali [ctb] (ORCID: <https://orcid.org/0000-0003-0132-8668>),
  Mark Viant [ths],
  Warwick Dunn [ths]
Maintainer: Thomas N. Lawson <thomas.nigel.lawson@gmail.com>
Built: R 4.6.0; ; 2026-04-29 23:42:36 UTC; windows
