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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "SpectraQL" in publications use:'
type: software
license: Artistic-2.0
title: 'SpectraQL: MassQL support for Spectra'
version: 1.6.0
doi: 10.1038/s41592-025-02660-z
identifiers:
- type: doi
  value: 10.32614/CRAN.package.SpectraQL
abstract: The Mass Spec Query Language (MassQL) is a domain-specific language enabling
  to express a query and retrieve mass spectrometry (MS) data in a more natural and
  understandable way for MS users. It is inspired by SQL and is by design programming
  language agnostic. The SpectraQL package adds support for the MassQL query language
  to R, in particular to MS data represented by Spectra objects. Users can thus apply
  MassQL expressions to analyze and retrieve specific data from Spectra objects.
authors:
- family-names: Rainer
  given-names: Johannes
  email: Johannes.Rainer@eurac.edu
  orcid: https://orcid.org/0000-0002-6977-7147
- family-names: Vicini
  given-names: Andrea
  email: andrea.vicini@eurac.edu
preferred-citation:
  type: article
  title: A universal language for finding mass spectrometry data patterns
  authors:
  - family-names: Damiani
    given-names: Tito
  - family-names: Jarmusch
    given-names: Alan K.
  - family-names: Aron
    given-names: Allegra T.
  - family-names: Petras
    given-names: Daniel
  - family-names: Phelan
    given-names: Vanessa V.
  - family-names: Zhao
    given-names: Haoqi Nina
  - family-names: Bittremieux
    given-names: Wout
  - family-names: Acharya
    given-names: Deepa D.
  - family-names: Ahmed
    given-names: Mohammed M. A.
  - family-names: Bauermeister
    given-names: Anelize
  - family-names: Bertin
    given-names: Matthew J.
  - family-names: Boudreau
    given-names: Paul D.
  - family-names: Borges
    given-names: Ricardo M.
  - family-names: Bowen
    given-names: Benjamin P.
  - family-names: Brown
    given-names: Christopher J.
  - family-names: Chagas
    given-names: Fernanda O.
  - family-names: Clevenger
    given-names: Kenneth D.
  - family-names: Correia
    given-names: Mario S. P.
  - family-names: Crandall
    given-names: William J.
  - family-names: Crüsemann
    given-names: Max
  - family-names: Fahy
    given-names: Eoin
  - family-names: Fiehn
    given-names: Oliver
  - family-names: Garg
    given-names: Neha
  - family-names: Gerwick
    given-names: William H.
  - family-names: Gilbert
    given-names: Jeffrey R.
  - family-names: Globisch
    given-names: Daniel
  - family-names: Gomes
    given-names: Paulo Wender P.
  - family-names: Heuckeroth
    given-names: Steffen
  - family-names: James
    given-names: C. Andrew
  - family-names: Jarmusch
    given-names: Scott A.
  - family-names: Kakhkhorov
    given-names: Sarvar A.
  - family-names: Kang
    given-names: Kyo Bin
  - family-names: Kessler
    given-names: Nikolas
  - family-names: Kersten
    given-names: Roland D.
  - family-names: Kim
    given-names: Hyunwoo
  - family-names: Kirk
    given-names: Riley D.
  - family-names: Kohlbacher
    given-names: Oliver
  - family-names: Kontou
    given-names: Eftychia E.
  - family-names: Liu
    given-names: Ken
  - family-names: Lizama-Chamu
    given-names: Itzel
  - family-names: Luu
    given-names: Gordon T.
  - family-names: Luzzatto Knaan
    given-names: Tal
  - family-names: Mannochio-Russo
    given-names: Helena
  - family-names: Marty
    given-names: Michael T.
  - family-names: Matsuzawa
    given-names: Yuki
  - family-names: McAvoy
    given-names: Andrew C.
  - family-names: McCall
    given-names: Laura-Isobel
  - family-names: Mohamed
    given-names: Osama G.
  - family-names: Nahor
    given-names: Omri
  - family-names: Neuweger
    given-names: Heiko
  - family-names: Niedermeyer
    given-names: Timo H. J.
  - family-names: Nishida
    given-names: Kozo
  - family-names: Northen
    given-names: Trent R.
  - family-names: Overdahl
    given-names: Kirsten E.
  - family-names: Rainer
    given-names: Johannes
    email: Johannes.Rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Reher
    given-names: Raphael
  - family-names: Rodriguez
    given-names: Elys
  - family-names: Sachsenberg
    given-names: Timo T.
  - family-names: Sanchez
    given-names: Laura M.
  - family-names: Schmid
    given-names: Robin
  - family-names: Stevens
    given-names: Cole
  - family-names: Subramaniam
    given-names: Shankar
  - family-names: Tian
    given-names: Zhenyu
  - family-names: Tripathi
    given-names: Ashootosh
  - family-names: Tsugawa
    given-names: Hiroshi
  - family-names: Hooft
    given-names: Justin J. J.
    name-particle: van der
  - family-names: Vicini
    given-names: Andrea
    email: andrea.vicini@eurac.edu
  - family-names: Walter
    given-names: Axel
  - family-names: Weber
    given-names: Tilmann
  - family-names: Xiong
    given-names: Quanbo
  - family-names: Xu
    given-names: Tao
  - family-names: Pluskal
    given-names: Tomáš
  - family-names: Dorrestein
    given-names: Pieter C.
  - family-names: Wang
    given-names: Mingxun
  journal: Nature Methods
  year: '2025'
  url: https://www.nature.com/articles/s41592-025-02660-z
  doi: 10.1038/s41592-025-02660-z
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/RforMassSpectrometry/SpectraQL
commit: 32f9d0b6306745ef40d8d09c40af4159dea8952a
url: https://github.com/RforMassSpectrometry/SpectraQL
date-released: '2026-04-28'
contact:
- family-names: Rainer
  given-names: Johannes
  email: Johannes.Rainer@eurac.edu
  orcid: https://orcid.org/0000-0002-6977-7147