To cite the SpectraQL package in publications use:

Damiani T, Jarmusch A, Aron A, Petras D, Phelan V, Zhao H, Bittremieux W, Acharya D, Ahmed M, Bauermeister A, Bertin M, Boudreau P, Borges R, Bowen B, Brown C, Chagas F, Clevenger K, Correia M, Crandall W, Crüsemann M, Fahy E, Fiehn O, Garg N, Gerwick W, Gilbert J, Globisch D, Gomes P, Heuckeroth S, James C, Jarmusch S, Kakhkhorov S, Kang K, Kessler N, Kersten R, Kim H, Kirk R, Kohlbacher O, Kontou E, Liu K, Lizama-Chamu I, Luu G, Luzzatto Knaan T, Mannochio-Russo H, Marty M, Matsuzawa Y, McAvoy A, McCall L, Mohamed O, Nahor O, Neuweger H, Niedermeyer T, Nishida K, Northen T, Overdahl K, Rainer J, Reher R, Rodriguez E, Sachsenberg T, Sanchez L, Schmid R, Stevens C, Subramaniam S, Tian Z, Tripathi A, Tsugawa H, van der Hooft J, Vicini A, Walter A, Weber T, Xiong Q, Xu T, Pluskal T, Dorrestein P, Wang M (2025). “A universal language for finding mass spectrometry data patterns.” Nature Methods. doi:10.1038/s41592-025-02660-z. https://www.nature.com/articles/s41592-025-02660-z.

Corresponding BibTeX entry:

  @Article{,
    title = {A universal language for finding mass spectrometry data
      patterns},
    author = {Tito Damiani and Alan K. Jarmusch and Allegra T. Aron and
      Daniel Petras and Vanessa V. Phelan and Haoqi Nina Zhao and Wout
      Bittremieux and Deepa D. Acharya and Mohammed M. A. Ahmed and
      Anelize Bauermeister and Matthew J. Bertin and Paul D. Boudreau
      and Ricardo M. Borges and Benjamin P. Bowen and Christopher J.
      Brown and Fernanda O. Chagas and Kenneth D. Clevenger and Mario
      S. P. Correia and William J. Crandall and Max Crüsemann and Eoin
      Fahy and Oliver Fiehn and Neha Garg and William H. Gerwick and
      Jeffrey R. Gilbert and Daniel Globisch and Paulo Wender P. Gomes
      and Steffen Heuckeroth and C. Andrew James and Scott A. Jarmusch
      and Sarvar A. Kakhkhorov and Kyo Bin Kang and Nikolas Kessler and
      Roland D. Kersten and Hyunwoo Kim and Riley D. Kirk and Oliver
      Kohlbacher and Eftychia E. Kontou and Ken Liu and Itzel
      Lizama-Chamu and Gordon T. Luu and Tal {Luzzatto Knaan} and
      Helena Mannochio-Russo and Michael T. Marty and Yuki Matsuzawa
      and Andrew C. McAvoy and Laura-Isobel McCall and Osama G. Mohamed
      and Omri Nahor and Heiko Neuweger and Timo H. J. Niedermeyer and
      Kozo Nishida and Trent R. Northen and Kirsten E. Overdahl and
      Johannes Rainer and Raphael Reher and Elys Rodriguez and Timo T.
      Sachsenberg and Laura M. Sanchez and Robin Schmid and Cole
      Stevens and Shankar Subramaniam and Zhenyu Tian and Ashootosh
      Tripathi and Hiroshi Tsugawa and Justin J. J. {van der Hooft} and
      Andrea Vicini and Axel Walter and Tilmann Weber and Quanbo Xiong
      and Tao Xu and Tomáš Pluskal and Pieter C. Dorrestein and Mingxun
      Wang},
    journal = {Nature Methods},
    year = {2025},
    url = {https://www.nature.com/articles/s41592-025-02660-z},
    doi = {10.1038/s41592-025-02660-z},
  }