Dataset Information

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 (MS) techniques are well-suited to high-throughput characterization of NP, 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.

SUBMITTER: Wang M

PROVIDER: S-EPMC5321674 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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

Wang Mingxun M Carver Jeremy J JJ Phelan Vanessa V VV Sanchez Laura M LM Garg Neha N Peng Yao Y Nguyen Don Duy DD Watrous Jeramie J Kapono Clifford A CA Luzzatto-Knaan Tal T Porto Carla C Bouslimani Amina A Melnik Alexey V AV Meehan Michael J MJ Liu Wei-Ting WT Crüsemann Max M Boudreau Paul D PD Esquenazi Eduardo E Sandoval-Calderón Mario M Kersten Roland D RD Pace Laura A LA Quinn Robert A RA Duncan Katherine R KR Hsu Cheng-Chih CC Floros Dimitrios J DJ Gavilan Ronnie G RG Kleigrewe Karin K Northen Trent T Dutton Rachel J RJ Parrot Delphine D Carlson Erin E EE Aigle Bertrand B Michelsen Charlotte F CF Jelsbak Lars L Sohlenkamp Christian C Pevzner Pavel P Edlund Anna A McLean Jeffrey J Piel Jörn J Murphy Brian T BT Gerwick Lena L Liaw Chih-Chuang CC Yang Yu-Liang YL Humpf Hans-Ulrich HU Maansson Maria M Keyzers Robert A RA Sims Amy C AC Johnson Andrew R AR Sidebottom Ashley M AM Sedio Brian E BE Klitgaard Andreas A Larson Charles B CB P Cristopher A Boya CAB Torres-Mendoza Daniel D Gonzalez David J DJ Silva Denise B DB Marques Lucas M LM Demarque Daniel P DP Pociute Egle E O'Neill Ellis C EC Briand Enora E Helfrich Eric J N EJN Granatosky Eve A EA Glukhov Evgenia E Ryffel Florian F Houson Hailey H Mohimani Hosein H Kharbush Jenan J JJ Zeng Yi Y Vorholt Julia A JA Kurita Kenji L KL Charusanti Pep P McPhail Kerry L KL Nielsen Kristian Fog KF Vuong Lisa L Elfeki Maryam M Traxler Matthew F MF Engene Niclas N Koyama Nobuhiro N Vining Oliver B OB Baric Ralph R Silva Ricardo R RR Mascuch Samantha J SJ Tomasi Sophie S Jenkins Stefan S Macherla Venkat V Hoffman Thomas T Agarwal Vinayak V Williams Philip G PG Dai Jingqui J Neupane Ram R Gurr Joshua J Rodríguez Andrés M C AMC Lamsa Anne A Zhang Chen C Dorrestein Kathleen K Duggan Brendan M BM Almaliti Jehad J Allard Pierre-Marie PM Phapale Prasad P Nothias Louis-Felix LF Alexandrov Theodore T Litaudon Marc M Wolfender Jean-Luc JL Kyle Jennifer E JE Metz Thomas O TO Peryea Tyler T Nguyen Dac-Trung DT VanLeer Danielle D Shinn Paul P Jadhav Ajit A Müller Rolf R Waters Katrina M KM Shi Wenyuan W Liu Xueting X Zhang Lixin L Knight Rob R Jensen Paul R PR Palsson Bernhard O BO Pogliano Kit K Linington Roger G RG Gutiérrez Marcelino M Lopes Norberto P NP Gerwick William H WH Moore Bradley S BS Dorrestein Pieter C PC Bandeira Nuno N

Nature biotechnology 20160801 8

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 (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Netwo ...[more]

PMID: 27504778

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Project description:Microorganisms produce a wide range of natural products (NPs) with clinically and agriculturally relevant biological activities. In bacteria and fungi, genes encoding successive steps in a biosynthetic pathway tend to be clustered on the chromosome as biosynthetic gene clusters (BGCs). Historically, "activity-guided" approaches to NP discovery have focused on bioactivity screening of NPs produced by culturable microbes. In contrast, recent "genome mining" approaches first identify candidate BGCs, express these biosynthetic genes using synthetic biology methods, and finally test for the production of NPs. Fungal genome mining efforts and the exploration of novel sequence and NP space are limited, however, by the lack of a comprehensive catalog of BGCs encoding experimentally-validated products. In this study, we generated a comprehensive reference set of fungal NPs whose biosynthetic gene clusters are described in the published literature. To generate this dataset, we first identified NCBI records that included both a peer-reviewed article and an associated nucleotide record. We filtered these records by text and homology criteria to identify putative NP-related articles and BGCs. Next, we manually curated the resulting articles, chemical structures, and protein sequences. The resulting catalog contains 197 unique NP compounds covering several major classes of fungal NPs, including polyketides, non-ribosomal peptides, terpenoids, and alkaloids. The distribution of articles published per compound shows a bias toward the study of certain popular compounds, such as the aflatoxins. Phylogenetic analysis of biosynthetic genes suggests that much chemical and enzymatic diversity remains to be discovered in fungi. Our catalog was incorporated into the recently launched Minimum Information about Biosynthetic Gene cluster (MIBiG) repository to create the largest known set of fungal BGCs and associated NPs, a resource that we anticipate will guide future genome mining and synthetic biology efforts toward discovering novel fungal enzymes and metabolites.

Dataset Information

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

Publications

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

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