ORCID Profile
0000-0001-6711-6719
Current Organisation
Centre National de la Recherche Scientifique
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Publisher: American Chemical Society (ACS)
Date: 11-02-2020
DOI: 10.1021/JACS.9B13786
Publisher: Springer Science and Business Media LLC
Date: 08-2016
DOI: 10.1038/NBT.3597
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: Springer Science and Business Media LLC
Date: 24-07-2019
Publisher: American Chemical Society (ACS)
Date: 13-11-2020
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.
Publisher: American Chemical Society (ACS)
Date: 13-04-2020
DOI: 10.26434/CHEMRXIV.12114987.V1
Abstract: Interpretation and annotation of fragmentation mass spectra strongly depends on our knowledge of collision-induced fragmentation mechanisms. Computational methods for interpretation of fragmentation operate in the boundaries of recognized fragmentation rules. The prevalence of non-sodiated fragment ions in sodiated ion fragmentation spectra is not yet fully recognized by the mass spectrometry community. Here, we investigated the extent of “Sodium Assisted Inductive Cleavage” (SAIC), a charge migration fragmentation occurring in the fragmentation spectra of sodiated precursors. The NIST17 fragmentation library was mined for evidence of SAIC. A substantial amount of fragment ions in sodiated precursor spectra can be linked to SAIC. Thus, this fragmentation mechanism must be considered to allow for accurate interpretation of fragmentation spectra.
Location: United States of America
Location: France
Location: No location found
No related grants have been discovered for Louis-Felix NOTHIAS.