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search DOI 10.1038/nbt.3597

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

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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Wang Mingxun, Carver Jeremy J., Phelan Vanessa V., Sanchez Laura M., Garg Neha, Peng Yao, Don duy Nguyen , 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, Dac-Trung nguyen , 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 (2016). Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology. 34 (8). 828-837. https://doi.org/10.1038/nbt.3597, https://archimer.ifremer.fr/doc/00408/51939/

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