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

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

• Document type: Journal article
• Source: NATURE BIOTECHNOLOGY; v. 34, n. 8, p. 828-837, AUG 2016.
• Web of Science Citations: 383

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. (AU)

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