The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data.

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. The FBMN method brings quantitative analyses, isomeric resolution, including from ion-mobility spectrometry, into molecular networks.

In polymicrobial infections, microbes can interact with both the host immune system and one another through direct contact or the secretion of metabolites, affecting disease progression and treatment options. The thick mucus in the lungs of patients with cystic fibrosis is highly susceptible to polymicrobial infections by opportunistic pathogens, including the bacterium Pseudomonas aeruginosa and the fungus Aspergillus fumigatus. Unravelling the hidden molecular interactions within such polymicrobial communities and their metabolic exchange processes will require effective enabling technologies applied to model systems. In the present study, MALDI-TOF and MALDI-FT-ICR imaging mass spectrometry (MALDI-IMS) combined with MS/MS networking were used to provide insight into the interkingdom interaction between P. aeruginosa and A. fumigatus at the molecular level. The combination of these technologies enabled the visualization and identification of metabolites secreted by these microorganisms grown on agar. A complex molecular interplay was revealed involving suppression, increased production, and biotransformation of a range of metabolites. Of particular interest is the observation that P. aeruginosa phenazine metabolites were converted by A. fumigatus into other chemical entities with alternative properties, including enhanced toxicities and the ability to induce fungal siderophores. This work highlights the capabilities of MALDI-IMS and MS/MS network analysis to study interkingdom interactions and provides insight into the complex nature of polymicrobial metabolic exchange and biotransformations. M icrobes that colonize mammalian hosts can form polymicrobial communities, such as biofilms, where they establish commensual, mutualistic, competitive, or antagonistic interactions with one another and with the host. In microbial disease, this complex interplay can affect the outcome of antimicrobial therapy (1). Therefore, it is important to understand polymicrobial populations and their interactions at the molecular level.In persons with cystic fibrosis (CF), the lungs are lined with a viscous mucus layer susceptible to polymicrobial infections (2). Pseudomonas aeruginosa, a Gram-negative bacterial opportunistic pathogen, is the most prevalent and persistent microorganism (3) isolated from the sputum of CF lungs and leading cause of mortality in CF patients (4). Within the CF lung, P. aeruginosa exists in biofilm-like macrocolonies (5) and is refractory to antimicrobial agents and the host immune response (6). Aspergillus fumigatus, an opportunistic fungal pathogen, is the second-most persistent microbe in the CF lung, with a 10-57% prevalence rate (3), and is capable of causing allergic bronchopulmonary aspergillosis (7).Superinfection with both P. aeruginosa and A. fumigatus in CF patients leads to decreased pulmonary function compared with monoinfection with either microbe (8). Interestingly, however, in a pulmonary mouse model, mice coinfected with P. aeruginosa and A. fumigatus had a higher survival rate than mice...