# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "mzR" in publications use:'
type: software
license: Artistic-2.0
title: 'mzR: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry
  data)'
version: 2.39.1
doi: 10.1038/nbt.2377
identifiers:
- type: doi
  value: 10.32614/CRAN.package.mzR
abstract: mzR provides a unified API to the common file formats and parsers available
  for mass spectrometry data. It comes with a subset of the proteowizard library for
  mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
authors:
- family-names: Neumann
  given-names: Steffen
  email: sneumann@ipb-halle.de
- family-names: Gatto
  given-names: Laurent
  email: laurent.gatto@uclouvain.be
- family-names: Kou
  given-names: Qiakng
  email: qkou@umail.iu.edu
preferred-citation:
  type: article
  title: A cross-platform toolkit for mass spectrometry and proteomics
  authors:
  - name: Chambers
  - family-names: C.
    given-names: Matthew
  - name: Maclean
  - name: Brendan
  - name: Burke
  - name: Robert
  - name: Amodei
  - name: Dario
  - name: Ruderman
  - family-names: L.
    given-names: Daniel
  - name: Neumann
  - name: Steffen
  - name: Gatto
  - name: Laurent
  - name: Fischer
  - name: Bernd
  - name: Pratt
  - name: Brian
  - name: Egertson
  - name: Jarrett
  - name: Hoff
  - name: Katherine
  - name: Kessner
  - name: Darren
  - name: Tasman
  - name: Natalie
  - name: Shulman
  - name: Nicholas
  - name: Frewen
  - name: Barbara
  - name: Baker
  - family-names: A.
    given-names: Tahmina
  - name: Brusniak
  - name: Mi-Youn
  - name: Paulse
  - name: Christopher
  - name: Creasy
  - name: David
  - name: Flashner
  - name: Lisa
  - name: Kani
  - name: Kian
  - name: Moulding
  - name: Chris
  - name: Seymour
  - family-names: L.
    given-names: Sean
  - name: Nuwaysir
  - family-names: M.
    given-names: Lydia
  - name: Lefebvre
  - name: Brent
  - name: Kuhlmann
  - name: Frank
  - name: Roark
  - name: Joe
  - name: Rainer
  - name: Paape
  - name: Detlev
  - name: Suckau
  - name: Hemenway
  - name: Tina
  - name: Huhmer
  - name: Andreas
  - name: Langridge
  - name: James
  - name: Connolly
  - name: Chadick
  - name: Trey
  - name: Holly
  - name: Krisztina
  - name: Eckels
  - name: Josh
  - name: Deutsch
  - family-names: W.
    given-names: Eric
  - name: Moritz
  - family-names: L.
    given-names: Robert
  - name: Katz
  - family-names: E.
    given-names: Jonathan
  - name: Agus
  - family-names: B.
    given-names: David
  - name: MacCoss
  - name: Michael
  - name: Tabb
  - family-names: L.
    given-names: David
  - name: Mallick
  - name: Parag
  year: '2012'
  journal: Nat Biotech
  doi: 10.1038/nbt.2377
  month: '10'
  issue: '10'
  volume: '30'
  url: http://dx.doi.org/10.1038/nbt.2377
  start: '918'
  end: '920'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/sneumann/mzR/issues/
commit: 3b07b8cfb326a3afceacc6a7d07c969acfceebd6
url: https://github.com/sneumann/mzR/
contact:
- family-names: Neumann
  given-names: Steffen
  email: sneumann@ipb-halle.de
references:
- type: article
  title: mzML - a Community Standard for Mass Spectrometry Data.
  authors:
  - family-names: Martens
    given-names: Lennart
  - family-names: Chambers
    given-names: Matthew
  - family-names: Sturm
    given-names: Marc
  - family-names: Kessner
    given-names: Darren
  - family-names: Levander
    given-names: Fredrik
  - family-names: Shofstahl
    given-names: Jim
  - family-names: Tang
    given-names: Wilfred H
  - family-names: Rompp
    given-names: Andreas
  - family-names: Neumann
    given-names: Steffen
  - family-names: Pizarro
    given-names: Angel D
  - family-names: Montecchi-Palazzi
    given-names: Luisa
  - family-names: Tasman
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    given-names: Eric W
  journal: Mol Cell Proteomics
  year: '2010'
  doi: 10.1074/mcp.R110.000133
- type: article
  title: A common open representation of mass spectrometry data and its application
    to proteomics research.
  authors:
  - family-names: Pedrioli
    given-names: Patrick G A
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  - family-names: McComb
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  - family-names: Paton
    given-names: Norman W
  - family-names: Simpson
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  - family-names: Taylor
    given-names: Chris F
  - family-names: Zhu
    given-names: Weimin
  - family-names: Aebersold
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  journal: Nat Biotechnol
  year: '2004'
  volume: '22'
  issue: '11'
  doi: 10.1038/nbt1031
  start: '1459'
  end: '1466'
- type: article
  title: A uniform proteomics MS/MS analysis platform utilizing open XML file formats.
  authors:
  - family-names: Keller
    given-names: Andrew
  - family-names: Eng
    given-names: Jimmy
  - family-names: Zhang
    given-names: Ning
  - family-names: Li
    given-names: Xiao-jun
  - family-names: Aebersold
    given-names: Ruedi
  journal: Mol Syst Biol
  year: '2005'
- type: article
  title: 'ProteoWizard: open source software for rapid proteomics tools development.'
  authors:
  - family-names: Kessner
    given-names: Darren
  - family-names: Chambers
    given-names: Matt
  - family-names: Burke
    given-names: Robert
  - family-names: Agus
    given-names: David
  - family-names: Mallick
    given-names: Parag
  journal: Bioinformatics
  year: '2008'
  volume: '24'
  issue: '21'
  doi: 10.1093/bioinformatics/btn323
  start: '2534'
  end: '2536'