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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 "mums2" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'mums2: Microbial Ecology by Tandem Mass Spectrometry'
version: 0.1.1
doi: 10.32614/CRAN.package.mums2
abstract: 'Tools that researchers can use to analyze untargeted metabolomics data
  generated using tandem mass spectroscopy from microbial communities. The overall
  approach taken to analyze metabolomics data parallels that used to analyze microbial
  communities using 16S rRNA gene sequencing data. Thus, we have a number of methods
  a user is able to use to generate data. Firstly, users can import Mass Spectrometry
  1(MS1) data and filter it. Users are then able to match Mass Spectrometry 2(MS2)
  data to the filtered (or unfiltered) MS1 data. With the matched data users are able
  to cluster it, annotate it, predict de novo chemical formulas and calculate alpha
  and beta diversity. For chemical formula predictions, this was the method used;
  "Towards de novo identification of metabolites by analyzing tandem mass spectra"
  (Sebastian Böcker, Florian Rasche (2008) <https://doi.org/10.1093/bioinformatics/btn270>).
  The similarity/dissimilarity calculations we used to cluster our data together was:
  "Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound
  identification" (Li, Y., Kind, T., Folz, J. et al. (2021) <https://doi.org/10.1038/s41592-021-01331-z>)
  and "Sharing and community curation of mass spectrometry data with Global Natural
  Products Social Molecular Networking" (Wang, M., Carver, J., Phelan, V. et al. (2021)
  <https://doi.org/10.1038/nbt.3597>).'
authors:
- family-names: Mason
  given-names: Allison
  email: masonar@umich.edu
  orcid: https://orcid.org/0000-0003-1339-1592
- family-names: Johnson
  given-names: Gregory
  email: grejoh@umich.edu
  orcid: https://orcid.org/0009-0008-3890-0297
- family-names: Schloss
  given-names: Patrick
  email: pschloss@umich.edu
  orcid: https://orcid.org/0000-0002-6935-4275
repository: https://mums2.r-universe.dev
repository-code: https://github.com/mums2/mums2
commit: e9742110baceb61791a2f07b85a4976605f02366
url: https://www.mums2.org/mums2/
date-released: '2026-06-11'
contact:
- family-names: Schloss
  given-names: Patrick
  email: pschloss@umich.edu
  orcid: https://orcid.org/0000-0002-6935-4275