Matches in Ghent University Academic Bibliography for { <https://biblio.ugent.be/publication/8628086> ?p ?o. }
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- 8628086 classification A1.
- 8628086 date "2019".
- 8628086 language "eng".
- 8628086 type journalArticle.
- 8628086 hasPart 8628087.pdf.
- 8628086 subject "Biology and Life Sciences".
- 8628086 doi "10.1128/msystems.00437-19".
- 8628086 issn "2379-5077".
- 8628086 issue "5".
- 8628086 volume "4".
- 8628086 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. IMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.".
- 8628086 author 088DB86C-F0EE-11E1-A9DE-61C894A0A6B4.
- 8628086 author 1734FE84-F0EE-11E1-A9DE-61C894A0A6B4.
- 8628086 author 2FC8151C-F0EE-11E1-A9DE-61C894A0A6B4.
- 8628086 author 32553A62-F0EE-11E1-A9DE-61C894A0A6B4.
- 8628086 author 54AE8E18-2240-11E3-BD2F-D1D610BDE39D.
- 8628086 author A11D3A4A-315A-11E4-9133-910EB5D1D7B1.
- 8628086 author DFFAFC4C-6887-11E5-AD70-3415B5D1D7B1.
- 8628086 author F3896850-297E-11E4-BFA2-63FCB4D1D7B1.
- 8628086 author F43CDE2E-F0ED-11E1-A9DE-61C894A0A6B4.
- 8628086 author F52F407E-F0ED-11E1-A9DE-61C894A0A6B4.
- 8628086 author F55ECBE6-F0ED-11E1-A9DE-61C894A0A6B4.
- 8628086 author F5C818B2-F0ED-11E1-A9DE-61C894A0A6B4.
- 8628086 author F830C8E2-F0ED-11E1-A9DE-61C894A0A6B4.
- 8628086 author F8C40A62-F0ED-11E1-A9DE-61C894A0A6B4.
- 8628086 dateCreated "2019-09-13T10:49:22Z".
- 8628086 dateModified "2024-12-12T16:27:01Z".
- 8628086 name "Introducing SPeDE : high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption-ionization time of flight mass spectrometry data".
- 8628086 pagination urn:uuid:85475878-fa30-4526-81c0-73ab36dbd0d8.
- 8628086 sameAs LU-8628086.
- 8628086 sourceOrganization urn:uuid:902de5f0-0a12-4558-9001-73c2fa46cc14.
- 8628086 sourceOrganization urn:uuid:d76817ca-74d1-4a3c-a353-f156416abfdb.
- 8628086 type A1.