Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Abstract

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.

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

“…This analysis defines spectral proximity between all MS/MS spectra of a dataset and visualizes them in a spectral network (Watrous et al, 2012). For the molecular annotation we compared the MS/MS spectra to a spectral library including the GNPS community contributed spectral library as well as Massbank, ReSpect, HMDB, and NIST14 (Forsythe and Wishart, 2009;Horai et al, 2010;Sawada et al, 2012;Stein, 2014;Wang et al, 2016). The overall goal of such an analysis is to enable robust, untargeted comparison of multiple samples at the molecular level.…”

“…After feature extraction from MS1, we calculated molecular formulas based on exact masses of individual and consensus features. In parallel, we performed clustering of identical MS/MS spectra and multiple spectra alignments using the Global Natural Product Social molecular networking (GNPS) (Wang et al, 2016). This analysis defines spectral proximity between all MS/MS spectra of a dataset and visualizes them in a spectral network (Watrous et al, 2012).…”

“…Besides dereplication of known compounds from the libraries, an additional multiple spectral alignment of all clustered spectra was performed. Thereby, all spectra are compared to each other using cosine similarity scoring (Stein and Scott, 1994) and spectrum-spectrum matches, with a cosine score higher or equal to 0.7 are connected as "nodes" in a network (Watrous et al, 2012;Wang et al, 2016). If nodes yielded a database hit during a spectrum library search, they can be labeled as specific compounds and nodes around the "hit" can be assumed to have similar chemical scaffolds.…”

“…With a medium resolution (R m/z 200 = 17.000), the iterative scan cycles result in several thousand spectra per sample. To reduce redundancy and computation time we clustered identical spectra to consensus spectra (Frank et al, 2008) and searched them against several spectral libraries, including GNPS (Wang et al, 2016), MassBank (Horai et al, 2010), ReSpect (Sawada et al, 2012) HMDB (Forsythe and Wishart, 2009), and NIST 2014 (Stein, 2014). Hereby a strict precursor mass tolerance of m/z 0.01 was used first, followed by a maximum allowed precursor delta mass of up to m/z 100, with the intention to annotate putative analogs.…”

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea

“…This genus has already yielded over 190 new NPs in the past two decades, accounting for more than 40% of all reported marine cyanobacterial NPs (8). The discovery of these NPs was mostly driven by classical isolation approaches, although this has been accelerated by the recent development of mass spectrometry (MS)-based molecular networking (groups metabolites according to their MS fragmentation fingerprints, simplifying the search for new NPs or their analogs) (9). Genomic analyses of these filamentous cyanobacteria have revealed that even well-studied strains possess additional genetic capacity to produce novel and chemically unique NPs (10), and suggest that bottom-up approaches (11) would be productive; a recent example is given by the discovery and description of the columbamides from Moorea bouillonii (12).…”