maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation.

Charlie Pauvert, David Wylensek, Selina Nüchtern, Thomas Clavel

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Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 authors.

Charlie PauvertFunctional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany.ORCID https://orcid.org/0000-0001-9832-2507

David WylensekFunctional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany.ORCID https://orcid.org/0000-0002-8424-5712

Selina NüchternFunctional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany.

Thomas ClavelFunctional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen 52074, Germany.ORCID https://orcid.org/0000-0002-7229-5595

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Motivation: Microbiologists use MALDI-TOF for fast and cheap identification of microbial isolates. However, most standard procedures rely on a commercial database. Bioinformatic tools to dereplicate MALDI-TOF spectra have been developed, but an open and resource-efficient tool to reduce the redundancy of microbial isolates is lacking. Here we develop "maldipickr" for de novo-clustering of MALDI-TOF spectra to dereplicate and select isolates, and thereby facilitate large-scale cultivation projects. Availability and implementation: The R package "maldipickr" is available through CRAN at https://doi.org/10.32614/CRAN.package.maldipickr along extensive documentation at https://clavellab.github.io/maldipickr.

Identifiers

PMID42381924

DOI10.1093/bioadv/vbag171

PMCPMC13317968

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.