Project description:Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.
Project description:Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
Project description:We performed RNA-seq analysis of control, NHR-23-depleted, SPE-44-depleted and NHR-23+SPE-44 depleted adult male animals, to identify genes regulated by NHR-23 and SPE-44.
Project description:Metabolome of Streptomyces sp. MBT84
Growth conditions: 5 days confluent on Minimal Medium agar supplemented with 1% glycerol, 0.5% mannitol and 25 mM TES
160- 165 = medium blank
166 - 171 = medium + catechol blank
172 - 177 = MBT84
178 - 183 = MBT84 + catechol
Project description:Molino, RJEJ., Rellin, KFB, Nellas, RB., Junio, HA. Small in size, big on taste: Metabolomics analysis of flavor compounds from Philippine garlic. PLoS ONE (2021) 16(5): e0247289. https://doi.org/10.1371/journal.pone.0247289
Project description:This is the molecular network done using ddMS files of QC pool sample analyzed with C18 (positive, negative polarities) and Zic-Hilic (Positive, negative polarities). DMSP was identified in cold-adapted Antarctic Ulva and its holobiont, and several other polar compounds were up-regulated during heat stress.
The full dataset can be found under the MassIVE Accession MSV000097253
Project description:Metabolic profiles of Actinobacteria isolated from a faecal sample that was taken from the intestinal tracts of a 28,000-year-old Siberian Mammoth. Strains have been grown on Nutrient Agar (Difco) for one week before metabolite extraction with ethyl acetate.
720-722: medium blank
723-725: Oerskovia sp. M15
726-728: Streptomyces sp. M19
729-731: Saccharopolyspora sp. M46
732-734: Streptomyces sp. M10
Project description:Man-made shallow fishponds in the Czech Republic have been facing a high eutrophication since 1950s. Anthropogenic eutrophication and feeding of fish have strongly affected the physico-chemical properties of water and its aquatic community composition leading to harmful algal bloom formation. In our current study, we have characterised the phytoplankton community across three hypertrophic ponds to assess the phytoplankton dynamics during the vegetation season. We microscopically identified and quantified 29 cyanobacterial taxa comprised of non-toxigenic and toxigenic species. Further, a detailed cyanopeptides (CNPs) profiling was performed using molecular networking analysis of liquid chromatography tandem mass spectrometry (LC MS/MS) data coupled with dereplication strategy. This MS networking approach led us to putatively identify forty CNPs: fourteen anabaenopeptins, ten microcystins, five cyanopeptolins, six microginins, two cyanobactins, a dipeptide radiosumin, a cyclooctapeptide planktocyclin and epidolastatin12. The combination of molecular networking and dereplication on online global natural product social networking (GNPS) web platform has proved as a valuable approach for rapid and simultaneous detection of high number of peptides, and rapidly assessing the risk for harmful bloom.