Feature-based molecular networking in the GNPS analysis environment

Nothias, Louis‐Félix; Petras, Daniel; Schmid, Robin; Dührkop, Kai; Rainer, Johannes Michael; Sarvepalli, Abinesh; Protsyuk, Ivan; Ernst, Madeleine; Tsugawa, Hiroshi; Fleischauer, Markus; Aicheler, Fabian; Aksenov, Alexander A.; Alka, Oliver; Allard, Pierre‐Marie; Barsch, Aiko; Cachet, Xavier; Caraballo‐Rodríguez, Andrés Mauricio; Silva, Ricardo R. da; Dang, Tam; Garg, Neha; Gauglitz, Julia M.; Gurevich, Alexey; Isaac, Giorgis; Jarmusch, Alan K.; Kameník, Zdeněk; Kang, Kyo Bin; Kessler, Nikolas; Koester, Irina; Korf, Ansgar; Gouellec, Audrey Le; Ludwig, Marcus; H, Christian Martin; McCall, Laura-Isobel; McSayles, Jonathan; Meyer, S.; Mohimani, Hosein; Morsy, Mustafa; Moyne, Oriane; Neumann, Steffen; Neuweger, Heiko; Nguyen, Ngoc Hung; Nothias-Esposito, Mélissa; Paolini, Julien; Phelan, Vanessa V.; Pluskal, Tomáš; Quinn, Robert A.; Rogers, Simon; Shrestha, Bindesh; Tripathi, Anupriya; Hooft, Justin J. J. van der; Vargas, Fernando; Weldon, Kelly C.; Witting, Michael; Yang, Heejung; Zhang, Zheng; Zubeil, Florian; Kohlbacher, Oliver; Böcker, Sebastian; Alexandrov, Theodore; Bandeira, Nuno; Wang, Mingxun; Dorrestein, Pieter C.

doi:10.1038/s41592-020-0933-6

Cited by 892 publications

(873 citation statements)

References 59 publications

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“…• Online informatics pipelines: GNPS Molecular Networking 12 / Library Search / MASST 14 / Feature-based Molecular Networking 15 , and MS2LDA.org 13 . As such, the Metabolomics Spectrum Resolver provides a universal interface to more than 450M MS/MS spectra from various public metabolomics repositories.…”

Section: Ms/ms Data Sources -Integration With Community Resourcesmentioning

confidence: 99%

Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service

Wang

Rogers

Bittremieux

et al. 2020

Preprint

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Section: Ms/ms Data Sources -Integration With Community Resourcesmentioning

confidence: 99%

Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service

Wang

Rogers

Bittremieux

et al. 2020

Preprint

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“…Thus, relevant detected peaks were aligned through Join Aligner Module considering 0.02 Da and retention time tolerance of 0.2 min. MGF file generated from MZmine 2.33 was uploaded to the Global Natural Products Social Molecular Networking online platform (GNPS) for generating a feature-based molecular network (https://ccms-ucsd.github.io/GNPSDocumentation/ featurebasedmolecularnetworking/) [19,60]. This molecular network was generated by filtering edges to have a cosine score above 0.70 and more than 4 matched peaks.…”

Section: Mzmine Preprocessing Workflow For Molecular Networkingmentioning

confidence: 99%

Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama

Atencio

et al. 2020

Marine Drugs

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The marine bacterial genus Pseudoalteromonas is known for their ability to produce antimicrobial compounds. The metabolite-producing capacity of Pseudoalteromonas has been associated with strain pigmentation; however, the genomic basis of their antimicrobial capacity remains to be explained. In this study, we sequenced the whole genome of six Pseudoalteromonas strains (three pigmented and three non-pigmented), with the purpose of identifying biosynthetic gene clusters (BGCs) associated to compounds we detected via microbial interactions along through MS-based molecular networking. The genomes were assembled and annotated using the SPAdes and RAST pipelines and mined for the identification of gene clusters involved in secondary metabolism using the antiSMASH database. Nineteen BGCs were detected for each non-pigmented strain, while more than thirty BGCs were found for two of the pigmented strains. Among these, the groups of genes of nonribosomal peptide synthetases (NRPS) that code for bromoalterochromides stand out the most. Our results show that all strains possess BGCs for the production of secondary metabolites, and a considerable number of distinct polyketide synthases (PKS) and NRPS clusters are present in pigmented strains. Furthermore, the molecular networking analyses revealed two new molecules produced during microbial interactions: the dibromoalterochromides D/D’ (11–12).

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“…Following non-targeted LC-MS/MS analysis of seawater PPL extracts, we obtained 5,521 MS1 ion features with assigned MS/MS spectra, which decreased to 4,384 MS1 ion features after PPL process blank subtraction (the feature matrix is provided in the supporting information). From these MS/MS spectra, we created a molecular network using the Feature-based Molecular Networking workflow in GNPS (Nothias et al, 2020;Wang et al, 2016). All MS/MS spectra were thereby searched against the GNPS, Massbank and NIST17 spectral reference libraries, which resulted in 92 annotations after blank subtraction (142 in total).…”

Section: Non-targeted Ms/ms Analysismentioning

confidence: 99%

“…Our results show a clear shift in the organic matter composition after the rain event that could be attributed in part to the increased presence of multiple anthropogenic pollutants, some from identifiable point sources. The results serve thereby as strong case for the use of non-targeted LC-MS/MS and advanced data-analysis methods such as Feature-based Molecular Networking, and the sharing and reuse of MS/MS datasets (Jarmusch et al, 2020;Nothias et al, 2020;Wang et al, 2020).…”

Section: Introductionmentioning

confidence: 96%

“…New developments in MS software tools, including molecular networking, comprehensive spectral and structure databases, statistical significance estimation, as well in silico annotation and community based annotation criteria have significantly improved the annotation of MS/MS spectra (Aron et al, 2019;Dührkop et al, 2019;Horai et al, 2010;Nothias et al, 2020;Ruttkies et al, 2016;Scheubert et al, 2017;Silva et al, 2018;Steen et al, 2020;Wang et al, 2016;Watrous et al, 2012). These technological improvements enable the annotation of a multitude of known and unknown chemical compounds which is central for a mechanistic understanding and prediction of how human actions influence ecosystems.…”

Section: Introductionmentioning

confidence: 99%

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Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

Petras

Minich

Cancelada

et al. 2020

Preprint

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Urbanization along coastlines alters marine ecosystems including contributing molecules of anthropogenic origin to the coastal dissolved organic matter (DOM) pool. A broad assessment of the nature and extent of anthropogenic impacts on coastal ecosystems is urgently needed to inform regulatory guidelines and ecosystem management. Recently, non-targeted tandem mass spectrometry approaches are gaining momentum for the analysis of global organic matter chemotypes including a wide array of natural and anthropogenic compounds. In line with these efforts, we developed a non-targeted liquid chromatography tandem mass spectrometry workflow that utilizes advanced data analysis approaches such as feature-based molecular networking and repository-scale spectrum searches. This workflow allows the scalable comparison and mapping of seawater chemotypes from large-scale spatial surveys as well as molecular family level annotation of unknown compounds. As a case study, we visualized organic matter chemotype shifts in coastal environments in northern San Diego, USA, after significant rain fall in winter 2017/2018 and highlight potential anthropogenic impacts. The observed seawater chemotype shifted significantly after a major rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, including pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa(methoxymethyl)melamine) and potential degradation products. By expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we further contextualized their possible origin and show their importance in other ecosystems. The mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which will contribute to a deliberate assessment of how chemical pollution impacts our oceans.<br>

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Feature-based molecular networking in the GNPS analysis environment

Cited by 892 publications

References 59 publications

Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service

Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service

Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama

Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

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