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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
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.
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https://hal-univ-rennes1.archives-ouvertes.fr/hal-01371824
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Submitted on : Monday, September 26, 2016 - 2:54:41 PM
Last modification on : Wednesday, October 14, 2020 - 4:21:39 AM

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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, Nature Publishing Group, 2016, 34 (8), pp.828-837. ⟨10.1038/nbt.3597⟩. ⟨hal-01371824⟩

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