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

Mingxun Wang (1) , Jeremy J. Carver (1) , Vanessa V. Phelan (2) , Laura M. Sanchez (2) , Neha Garg (2) , Yao Peng , Don Duy Nguyen (3) , Jeramie Watrous , Clifford A. Kapono , Tal Luzzatto-Knaan , Carla Porto , Amina Bouslimani , Alexey V. Melnik , Michael J. Meehan , Wei-Ting Liu (4) , Max Crüsemann , Paul D. Boudreau , Eduardo Esquenazi , Mario Sandoval-Calderon , Roland D. Kersten , Laura A. Pace , Robert A. Quinn , Katherine R. Duncan , Cheng-Chih Hsu , Dimitrios J. Floros , Ronnie G. Gavilan , Karin Keligrewe , Trent Northen , Rachel J. Dutton , Delphine Parrot (5) , Erin E. Carlson , Bertrand Aigle (6) , Charlotte F. Michelsen , Lars Jelsbak , Christian Sohlenkamp , Pavel Pevzner , Anna Edlund , Jeffrey Mclean , Jörn Piel (7) , Brian T. Murphy , Lena Gerwick , Chih-Chuang Liaw , Yu-Liang Yang (8) , Hans-Ulrich Humpf , Maria Maansson , Robert A. Keyzers , Amy C. Sims , Andrew R. Johnson , Ashley M. Sidebottom , Briand E. Sedio , Andreas Klitgaare , Charles B. Larson , Cristopher A. Boya P. , Daniel Torres-Mendoza , David J. Gonzalez , Denise B. Silva , Lucas M. Marques , Daniel P. Demarque , Egle Pociute , Ellis C. O’neil , Enora Briand (9) , Eric J.N. Helfrich (7) , Eve A. Granotosky , Evgenia Glukhov , Florian Ryffel , Hailey Houson , Hosein Mohimani , Jenan J. Kharbush , Yi Zeng , Julia A. Vorholt , Kenji L. Kurita , Pep Charusanti , Kerry L. Mcphail , Kristian Fog Nielsen , Lisa Vuong , Maryam Elfeki , Matthew F. Traxler , Niclas Engene , Nobuhiro Koyama , Oliver B. Vining , Ralph Baric , Ricardo R. Silva (10) , Samantha J. Mascuch , Sophie Tomasi (5) , Stefan Jenkins (11) , Venkat Macherla , Thomas Hoffman , Vinayak Agarwal , Philip G. Williams , Jingqui Dai , Ram Neupane , Joshua Gurr , Andrés M.C. Rodriguez , Anne Lamsa , Chen Zhang (12) , Kathleen Dorrestein , Brendan M. Duggan , Jehad Almaliti , Pierre-Marie Allard , Prasad Phapale , Louis-Felix Nothias , Theorodore Alexandrov , Marc Litaudon (13) , Jean-Luc Wolfender , Jennifer E. Kyle , Thomas O. Metz , Tyloer Peryea , Dac-Trung Nguyen (3) , Danielle Vanleer , Paul Shinn , Ajit Jadhav , Rolf Müller , Katrina M. Waters , Wenyuan Shi , Xueting Liu , Lixin Zhang (14) , Rob Knight , Paul R. Jensen (15) , Bernhard Ø Palsson , Kit Pogliano , Roger G. Linington , Marcelino Gutierrez , Norberto P. Lopes , William H. Gerwick (16) , Bradley S. Moore , Pieter C. Dorrestein (16) , Nuno Bandeira

1 Computer Science and Engineering
2 Collaborative Mass Spectrometry Innovation Center
3 KDDI R&D Laboratories Inc. [Saitama]
4 Shandong University of Science and Technology
5 ISCR - Institut des Sciences Chimiques de Rennes
6 DynAMic - Dynamique des Génomes et Adaptation Microbienne
7 ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich]
8 Metacohorts Consortium
9 ECOBIO - Ecosystèmes, biodiversité, évolution [Rennes]
10 UNICAMP - Universidade Estadual de Campinas = University of Campinas
11 UMPhy CNRS/THALES - Unité mixte de physique CNRS/Thales
12 Department of Civil Engineering
13 ICSN - Institut de Chimie des Substances Naturelles
14 IRCELYON - Institut de recherches sur la catalyse et l'environnement de Lyon
15 Phys-ENS - Laboratoire de Physique de l'ENS Lyon
16 Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego]

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.

Keywords: Knowledge based systems; Spectrometry; Tandem mass; Open Access; Natural products; Ms libraries; Mass spectrometry data; Knowledge base; High through-put characterization; Data driven; Mass spectrometry

Domains: Life Sciences [q-bio]; Ecology, environment

Mingxun Wang, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, et al.. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 2016, 34 (8), pp.828-837. ⟨10.1038/nbt.3597⟩. ⟨hal-01371824⟩