spectratoqueries

Repository to translate spectra to queries

https://github.com/spectra-to-knowledge/spectratoqueries

Science Score: 67.0%

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CITATION.cff file
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DOI references
Found 18 DOI reference(s) in README
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Links to: nature.com
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Low similarity (13.5%) to scientific vocabulary

Keywords

knowledge-extraction monoterpene-indole-alkaloids querying-system spectral-information spectral-library tandem-ms

Last synced: 6 months ago · JSON representation ·

Repository

Repository to translate spectra to queries

Basic Info

Host: GitHub
Owner: spectra-to-knowledge
License: agpl-3.0
Language: R
Default Branch: main
Homepage: https://spectra-to-knowledge.github.io/SpectraToQueries/
Size: 3.34 MB

Statistics

Stars: 1
Watchers: 1
Forks: 1
Open Issues: 0
Releases: 0

Topics

knowledge-extraction monoterpene-indole-alkaloids querying-system spectral-information spectral-library tandem-ms

Created about 2 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation Codemeta

SpectraToQueries

Repository to translate spectra to queries.

Requirements

Here is what you minimally need:

A file containing MS/MS spectra with associated skeleton information (or any other relevant chemical classification) provided as metadata. This structure information, stored in the metadata field “skeleton”, allows the generation of queries specific to a given skeleton by extracting repetitive skeleton-specific fragmentation patterns. The MIADB file is provided as an example.

Installation

As the package is not (yet) available on CRAN, you will need to install with:

r install.packages( "SpectraToQueries", repos = c( "https://spectra-to-knowledge.r-universe.dev", "https://bioc.r-universe.dev", "https://cloud.r-project.org" ) )

Use

To reproduce the example that uses the Monoterpene Indole Alkaloids Database (.mgf) file by default, which includes the annotation of spectral skeletons:

r SpectraToQueries::spectra_to_queries()

To reproduce the “grouped” example that uses the MIADB file, which includes an expert-based annotation of spectral “super skeletons” (combination of skeletons exhibiting a high structural similarity):

r SpectraToQueries::spectra_to_queries( spectra = system.file( "extdata", "spectra_grouped.rds", package = "SpectraToQueries" ), export = "data/interim/queries-grouped.tsv" )

To generate diagnostic ions queries from your spectra:

r SpectraToQueries::spectra_to_queries( spectra = "yourAwesomeSpectra.mgf", export = "path/yourEvenBetterResults.tsv" )

Showing all parameters:

r SpectraToQueries::spectra_to_queries( spectra = NULL, export = "data/interim/queries.tsv", beta_1 = 1.0, beta_2 = 0.5, dalton = 0.01, decimals = 4L, intensity_min = 0.0, ions_max = 10L, n_skel_min = 5L, n_spec_min = 3L, ppm = 30.0, fscore_min = 0.0, precision_min = 0.0, recall_min = 0.0, zero_val = 0.0 )

Main Citations

Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids: https://doi.org/10.1186/s13321-025-01009-0

Additional software credits

| Package | Version | Citation | |:---|:---|:---| | base | 4.5.1 | R Core Team (2025) | | BiocGenerics | 0.55.1 | Huber et al. (2015) | | BiocManager | 1.30.26 | Morgan and Ramos (2025) | | BiocParallel | 1.43.4 | Wang et al. (2025) | | BiocVersion | 3.22.0 | Morgan (2025) | | knitr | 1.50 | Xie (2014); Xie (2015); Xie (2025) | | MsBackendMgf | 1.17.0 | Gatto, Rainer, and Gibb (2025) | | pkgload | 1.4.0 | Wickham et al. (2024) | | rmarkdown | 2.29 | Xie, Allaire, and Grolemund (2018); Xie, Dervieux, and Riederer (2020); Allaire et al. (2024) | | Spectra | 1.19.4 | Rainer et al. (2022) | | testthat | 3.2.3 | Wickham (2011) | | tidytable | 0.11.2 | Fairbanks (2024) | | tidyverse | 2.0.0 | Wickham et al. (2019) |

Allaire, JJ, Yihui Xie, Christophe Dervieux, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, et al. 2024. *rmarkdown: Dynamic Documents for r*. .

Fairbanks, Mark. 2024. *tidytable: Tidy Interface to “data.table”*. .

Gatto, Laurent, Johannes Rainer, and Sebastian Gibb. 2025. *MsBackendMgf: Mass Spectrometry Data Backend for Mascot Generic Format (Mgf) Files*. .

Huber, W., Carey, V. J., Gentleman, R., Anders, et al. 2015. “Orchestrating High-Throughput Genomic Analysis with Bioconductor.” *Nature Methods* 12 (2): 115–21. .

Morgan, Martin. 2025. *BiocVersion: Set the Appropriate Version of Bioconductor Packages*. .

Morgan, Martin, and Marcel Ramos. 2025. *BiocManager: Access the Bioconductor Project Package Repository*. .

R Core Team. 2025. *R: A Language and Environment for Statistical Computing*. Vienna, Austria: R Foundation for Statistical Computing. .

Rainer, Johannes, Andrea Vicini, Liesa Salzer, Jan Stanstrup, Josep M. Badia, Steffen Neumann, Michael A. Stravs, et al. 2022. “A Modular and Expandable Ecosystem for Metabolomics Data Annotation in r.” *Metabolites* 12: 173. .

Wang, Jiefei, Martin Morgan, Valerie Obenchain, Michel Lang, Ryan Thompson, and Nitesh Turaga. 2025. *BiocParallel: Bioconductor Facilities for Parallel Evaluation*. .

Wickham, Hadley. 2011. “testthat: Get Started with Testing.” *The R Journal* 3: 5–10. .

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” *Journal of Open Source Software* 4 (43): 1686. .

Wickham, Hadley, Winston Chang, Jim Hester, and Lionel Henry. 2024. *pkgload: Simulate Package Installation and Attach*. .

Xie, Yihui. 2014. “knitr: A Comprehensive Tool for Reproducible Research in R.” In *Implementing Reproducible Computational Research*, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC.

———. 2015. *Dynamic Documents with R and Knitr*. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. .

———. 2025. *knitr: A General-Purpose Package for Dynamic Report Generation in R*. .

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. *R Markdown: The Definitive Guide*. Boca Raton, Florida: Chapman; Hall/CRC. .

Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. *R Markdown Cookbook*. Boca Raton, Florida: Chapman; Hall/CRC. .

Owner

Name: spectra-to-knowledge
Login: spectra-to-knowledge
Kind: organization

Repositories: 1
Profile: https://github.com/spectra-to-knowledge

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "SpectraToQueries" in publications use:'
type: software
license: AGPL-3.0-or-later
title: 'SpectraToQueries: Spectra to queries'
version: 0.0.0.9001
abstract: SpectraToQueries provides the infrastructure to translate spectra to queries.
authors:
- family-names: Rutz
  given-names: Adriano
  email: adafede@gmail.com
  orcid: https://orcid.org/0000-0003-0443-9902
preferred-citation:
  type: manual
  title: 'SpectraToQueries: SpectraToQueries provides the infrastructure to translate
    spectra to queries'
  authors:
  - family-names: Rutz
    given-names: Adriano
    email: adafede@gmail.com
    orcid: https://orcid.org/0000-0003-0443-9902
  - family-names: Szwarc
    given-names: Sarah
    email: sarah.szwarc@universite-paris-saclay.fr
    orcid: https://orcid.org/0000-0001-6369-5522
  year: '2025'
  notes: R package, version 0.0.9001
repository: https://bioconductor.org/
repository-code: https://github.com/spectra-to-knowledge/spectra-to-queries
url: https://spectra-to-knowledge.github.io/SpectraToQueries
contact:
- family-names: Rutz
  given-names: Adriano
  email: adafede@gmail.com
  orcid: https://orcid.org/0000-0003-0443-9902
keywords:
- knowledgeExtraction
- spectralInformation
- queryingSystem
- knowledge-extraction
- monoterpene-indole-alkaloids
- querying-system
- spectral-information
- spectral-library
- tandem-ms
references:
- type: article
  title: 'Translating community-wide spectral library into actionable chemical knowledge:
    a proof of concept with monoterpene indole alkaloids'
  authors:
  - family-names: Szwarc
    given-names: Sarah
    orcid: https://orcid.org/0000-0001-6369-5522
  - family-names: Rutz
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  - family-names: Hazni
    given-names: Hazrina
  - family-names: Jagora
    given-names: Adrien
  - family-names: Mbeng Obame
    given-names: Rany B
  - family-names: Jin Kyoung
    given-names: Noh
  - family-names: Otogo N'Nang
    given-names: Elvis
  - family-names: Alaribe
    given-names: Stephenie C
  - family-names: Awang
    given-names: Khalijah
  - family-names: Bernadat
    given-names: Guillaume
  - family-names: Choi
    given-names: Young Hae
  - family-names: Courdavault
    given-names: Vincent
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  - family-names: Gaslonde
    given-names: Thomas
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    name-particle: van der
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    given-names: Kyo Bin
  - family-names: Le Pogam
    given-names: Pierre
  - family-names: Beniddir
    given-names: Mehdi A
    orcid: https://orcid.org/0000-0003-2153-4290
  journal: J. Cheminform.
  year: '2025'
  volume: '17'
  url: https://doi.org/10.1186/s13321-025-01009-0
  keywords:
  - Expert knowledge
  - MS/MS
  - Monoterpene indole alkaloids
  - Query
  - Scaffold
  - Similarity
  doi: 10.1186/s13321-025-01009-0
  issn: 1758-2946
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  authors:
  - family-names: Morgan
    given-names: Martin
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  - family-names: Wang
    given-names: Jiefei
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Lang
    given-names: Michel
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  - family-names: Thompson
    given-names: Ryan
    email: rct@thompsonclan.org
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    given-names: Nitesh
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CodeMeta (codemeta.json)

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.github/workflows/R-CMD-check.yaml actions

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.github/workflows/update-citation-cff.yaml actions

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DESCRIPTION cran

R >= 4.3.0 depends
BiocGenerics >= 0.48.1 imports
MsBackendMgf >= 1.10.0 imports
Spectra >= 1.12.0 imports
furrr >= 0.3.1 imports
progressr >= 0.15.0 imports
tibble >= 3.2.1 imports
tidytable >= 0.11.1 imports
BiocManager * suggests
R.utils * suggests
knitr * suggests
spelling * suggests
testthat * suggests

ecosyste.ms

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