ABSTRACT: MS/MS spectra of bacterial culture extracts were acquired on Orbitrap Exploris 120 mass spectrometer in negative mode. Data was converted to mzML for Classical Molecular Networking on GNPS.
INSTRUMENT(S): Orbitrap Exploris 120 mass spectrometer
Project description:Liquid bacterial monocultures for 16 cheese rind microbiome derived Actinobacteria isolates were performed in Brain Heart Infusion (BHI) medium for 7 days and extracted using Amberlite XAD16 resin followed by methanol. Extracts were analyzed via LC-MS/MS and blank MS/MS spectra were removed using BLANKA2 with an eps value of 0.1 for GNPS classical molecular networking analysis.
Project description:LC-MS/MS dataset containing blank and sample acquisitions used to benchmark performance of blank removal using BLANKA2 and GNPS classical molecular networking. Each dataset contains 5 sets of output data from BLANKA2 in which the eps values were set to 0.1, 0.3, 0.5, 0.7, and 0.9 for output directories with suffixes 1, 2, 3, 4, and 5, respectively.
Project description:Tandem MS data used for GNPS networking and analysis. The samples included in this data set are fractions (A-G) from a bacterial extraction of PA14 with or without exposure to TLCA. There are also two controls: extractions from media exposed to TLCA and media alone. All fractions were analyzed in triplicate therefore each fraction has file raw files.
Project description:6 days old Arabidopsis thaliana of Col-0 wild-type and 35S:ARR1-SRDX transgenic seedlings grown in liquid culture (1/2 MS, 1 g/L sucrose, 0.5 g/L MES, pH 5.7) were induced with either 5 µM 6-Benzyladenine (a cytokinin analog) for 15 or 120 min, or mock-treated 120 min as a control. These samples were subjected to microarray analysis.
Project description:Dataset 1 contains bacterial-fungal monocultures and tripartite co-cultures in which Scopulariopsis sp. JB370 are grown with 1) Hafnia alvei JB232 and 2) Pseudomonas psychrophila JB418 or Escherichia coli K12. Dataset 2 contains bacterial-fungal tripartite co-cultures in which Penicillium solitum #12 are grown with 1) Glutamicibacter arilaitensis JB182 or Brevibacterium linens JB5 and 2) Pseudomonas psychrophila JB418 or Escherichia coli K12. All cultures from each dataset were grown on 10% cheese curd agar (CCA) and extracted using acetonitrile. Extracts were analyzed via LC-MS(/MS) and processed with MZmine2 for analysis with MetaboAnalyst 5.0 and GNPS feature based molecular networking.
Project description:<p>The history of lichen compound identification has long relied on techniques such as spot tests and TLC, which have been surpassed in sensitivity and accuracy by modern metabolomic techniques such as high-resolution MS/MS. In 2019, Olivier-Jimenez et al. released the Lichen DataBase (LDB), a library containing the Q-TOF MS/MS spectra of 251 metabolites on the GNPS and MetaboLights platforms, that has been widely used for the identification of lichen-derived unknowns. To increase the compound coverage, we have generated the Orbitrap MS/MS spectra of a further 534 lichen-derived compounds from the metabolite library of Jack Elix, housed at the CANB herbarium (Canberra, Australia). This included 399 unique metabolites that are not in the LDB, bringing the total number combined to 650. Technical validation was achieved by investigating the compounds in three Australian lichen extracts using the Library Search and Molecular Networking tools on the GNPS platform. This update provides a much larger database for lichen compound identification, which we envisage will allow refining of the chemotaxonomy framework and contribute to compound discovery.</p>
Project description:Liquid bacterial monocultures for 16 cheese rind microbiome derived Actinobacteria isolates were performed in Brain Heart Infusion (BHI) medium for 7 days and extracted using Amberlite XAD16 resin followed by methanol. Extracts were analyzed via LC-MS/MS and blank MS/MS spectra were removed using BLANKA2 with an eps value of 0.1 for GNPS classical molecular networking analysis.