ORCID Profile
0000-0002-3105-1359
Current Organisations
University of Antwerp
,
University of California, San Diego
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Publisher: Cold Spring Harbor Laboratory
Date: 15-05-2022
DOI: 10.1101/2022.05.15.490691
Abstract: Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of public MS/MS spectra. Annotations were propagated based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative ex les of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 09-2019
Publisher: Oxford University Press (OUP)
Date: 26-10-2013
DOI: 10.1093/BIB/BBT074
Publisher: Springer Science and Business Media LLC
Date: 03-09-2018
Publisher: American Chemical Society (ACS)
Date: 24-07-2014
DOI: 10.1021/PR401269Z
Abstract: Spectral library searching is a popular approach for MS/MS-based peptide identification. Because the size of spectral libraries continues to grow, the performance of searching algorithms is an important issue. This technical note introduces a strategy based on a minimum shared peak count between two spectra to reduce the set of admissible candidate spectra when issuing a query. A theoretical validation through time complexity analysis and an experimental validation based on an implementation of the candidate reduction strategy show that the approach can achieve a reduction of the set of candidate spectra by (at least) an order of magnitude, resulting in a significant improvement in the speed of the search. Meanwhile, more than 99% of the positive search results is retained. This efficient strategy to drastically improve the speed of spectral library searching with a negligible loss of sensitivity can be applied to any current spectral library search tool, irrespective of the employed similarity metric.
Publisher: Cold Spring Harbor Laboratory
Date: 10-05-2020
DOI: 10.1101/2020.05.09.086066
Abstract: The growth of online mass spectrometry metabolomics resources, including data repositories, spectral library databases, and online analysis platforms has created an environment of online/web accessibility. Here, we introduce the Metabolomics Spectrum Resolver ( metabolomics-usi.ucsd.edu/ ), a tool that builds upon these exciting developments to allow for consistent data export (in human and machine-readable forms) and publication-ready visualisations of tandem mass spectrometry spectra. This tool supports the Human Proteome Organization – Proteomics Standards Initiative’s Universal Spectrum Identifier (USI) specification, which has been extended to deal with the metabolomics use cases. To date, this resource already supports data formats from GNPS, MassBank, MS2LDA, MassIVE, MetaboLights, and Metabolomics Workbench and is integrated into several of these resources.
Publisher: Springer Science and Business Media LLC
Date: 28-11-2022
DOI: 10.1038/S41564-022-01266-X
Abstract: Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and h ers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a erse set of 880 microbial community s les collected for the Earth Microbiome Project. We include licon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore ersity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite ersity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for ex le, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from erse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
Location: United States of America
No related grants have been discovered for Wout Bittremieux.