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:Identification of features using ddMS acquisition on QC pool samples
Survey of MS/MS spectra using molecular networking to check for peak matching
Project description:Combined water, methanol and chloroform soil extracts from week 12 of a California grassland soil root detritus experiment conducted under normal (~16% GWC) and reduced moisture (~8% GWC) conditions.
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