ArticlemSystems2019
Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.
Article in mSystems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.Gut microbes · 2026Article
- IDBac: an open-access web platform to identify bacteria and analyze relationships in culture collections using MALDI-TOF mass spectrometry.Nature communications · 2026Article
- Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science.The ISME journal · 2026Article
- maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation.Bioinformatics advances · 2026Article
- Characterization of isolates used in bacterial-based strategies for accelerated carbonation of lime mortars.Applied and environmental microbiology · 2025Article
- IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry.bioRxiv : the preprint server for biology · 2025Article
- OralPathogens (Basel, Switzerland) · 2024Article
- NovelMicrobiology spectrum · 2024Article
- Refermentation and maturation of lambic beer in bottles: a necessary step for gueuze production.Applied and environmental microbiology · 2024Article
- Review
- Review
- A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont.Animal microbiome · 2023Article
- Artificial intelligence in microbial natural product drug discovery: current and emerging role.Natural product reports · 2022Review
- Article
- Classification of Environmental Strains from Order to Genus Levels Using Lipid and Protein MALDI-ToF Fingerprintings and Chemotaxonomic Network Analysis.Microorganisms · 2022Article
- Automated Microbial Library Generation Using the Bioinformatics Platform IDBac.Molecules (Basel, Switzerland) · 2022Article
- Article
- Genomic Aromatic Compound Degradation Potential of NovelInternational journal of molecular sciences · 2021Article
- Development of an NMR-Based Platform for the Direct Structural Annotation of Complex Natural Products Mixtures.Journal of natural products · 2021Article
- Innovations to culturing the uncultured microbial majority.Nature reviews. Microbiology · 2021Review
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDE
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