maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation

Summary: Microbiologists use MALDI-TOF for fast and cheap identification of microbial isolates. However, the standard procedure relies 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. Code and data to reproduce the analysis and figure are available at https://github.com/ClavelLab/maldipickr_manuscript and https://zenodo.org/records/15744631.