Reproducible Molecular Networking Of Untargeted Mass Spectrometry Data Using GNPS.

Abstract

Herein, we present a protocol for the use of Global Natural Products Social (GNPS) Molecular Networking, an interactive online chemistry-focused mass spectrometry data curation and analysis infrastructure. The goal of GNPS is to provide as much chemical insight for an untargeted tandem mass spectrometry data set as possible and to connect this chemical insight to the underlying biological questions a user wishers to address. This can be performed within one experiment or at the repository scale. GNPS not only serves as a public data repository for untargeted tandem mass spectrometry data with the sample information (metadata), it also captures community knowledge that is disseminated via living data across all public data. One or the main analysis tools used by the GNPS community is molecular networking. Molecular networking creates a structured data table that reflects the chemical space from tandem mass spectrometry experiments via computing the relationships of the tandem mass spectra through spectral similarity. This protocol provides step-by-step instructions for creating reproducible high-quality molecular networks. For training purposes, the reader is led through the protocol from recalling a public data set and its sample information to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

Antioxidant, Anti-Inflammatory, and Anti-Apoptotic Effects of Azolla pinnata Ethanolic Extract against Lead-Induced Hepatotoxicity in Rats

“…Out of 89 metabolites, only 22 were identified based on the molecular networking database. Eight metabolites were found to be reliable and are considered, as shown in Table 1 [ 44 ].…”

“…These findings were in line with those of Debashis et al (2016) [ 21 ], who reported that A. pinnata reduces serum activities of ALT and AST. The ameliorative effects of A. pinnata against lead acetate-induced hepatotoxicity may be attributed to the antioxidant and anti-inflammatory activities of its constituents as 10 metabolites were found to be reliable ( Figure 3 and Figure 4 , Table 1 ) [ 44 ]. A. pinnata ethanolic extract was found to be rich in flavonoids, which are well-known for their antioxidant and anti-inflammatory activities [ 68 ].…”

Reference data based insights expand understanding of human metabolomes

“…These examples highlight how molecular networking can be used to propagate potential metabolism. How potential metabolism can be inferred with molecular networking is explained in (Quinn et al, 2017) and (Aron et al, 2020).…”

Analytical and Computational Advances, Opportunities, and Challenges in Marine Organic Biogeochemistry in an Era of “Omics”

“…Several computational tools increase our ability to identify unknown compounds through searches and in silico calculations (CSI:FingerID, Dührkop et al, 2019;ClassyFire, Feunang et al, 2016;MetFrag, Ruttkies et al, 2019). The structural similarities in MS 2 spectra have proven especially useful in identifying compounds (MolNetEnhancer, Ernst et al, 2019;MetDNA, Shen et al, 2019;MS2LDA, van der Hooft et al, 2020), which is evident in the expanded list of tools now available at Global Natural Products Social Networking (Wang et al, 2016;Aron et al, 2020). For example, users can search mass spectrometry data using MASST (Wang et al, 2020) and reuse publicly available data via ReDU (Jarmusch et al, 2019).…”