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

Wang, Mingxun and Carver, Jeremy J and Phelan, Vanessa V and Sanchez, Laura M and Garg, Neha and Peng, Yao and Nguyen, Don Duy and Watrous, Jeramie and Kapono, Clifford A and Luzzatto-Knaan, Tal and Porto, Carla and Bouslimani, Amina and Melnik, Alexey V and Meehan, Michael J and Liu, Wei-Ting and Crüsemann, Max and Boudreau, Paul D and Esquenazi, Eduardo and Sandoval-Calderón, Mario and Kersten, Roland D and Pace, Laura A and Quinn, Robert A and Duncan, Katherine R and Hsu, Cheng-Chih and Floros, Dimitrios J and Gavilan, Ronnie G and Kleigrewe, Karin and Northen, Trent and Dutton, Rachel J and Parrot, Delphine and Carlson, Erin E and Aigle, Bertrand and Michelsen, Charlotte F and Jelsbak, Lars and Sohlenkamp, Christian and Pevzner, Pavel and Edlund, Anna and McLean, Jeffrey and Piel, Jörn and Murphy, Brian T and Gerwick, Lena and Liaw, Chih-Chuang and Yang, Yu-Liang and Humpf, Hans-Ulrich and Maansson, Maria and Keyzers, Robert A and Sims, Amy C and Johnson, Andrew R and Sidebottom, Ashley M and Sedio, Brian E and Klitgaard, Andreas and Larson, Charles B and Boya P, Cristopher A and Torres-Mendoza, Daniel and Gonzalez, David J and Silva, Denise B and Marques, Lucas M and Demarque, Daniel P and Pociute, Egle and O'Neill, Ellis C and Briand, Enora and Helfrich, Eric J N and Granatosky, Eve A and Glukhov, Evgenia and Ryffel, Florian and Houson, Hailey and Mohimani, Hosein and Kharbush, Jenan J and Zeng, Yi and Vorholt, Julia A and Kurita, Kenji L and Charusanti, Pep and McPhail, Kerry L and Nielsen, Kristian Fog and Vuong, Lisa and Elfeki, Maryam and Traxler, Matthew F and Engene, Niclas and Koyama, Nobuhiro and Vining, Oliver B and Baric, Ralph and Silva, Ricardo R and Mascuch, Samantha J and Tomasi, Sophie and Jenkins, Stefan and Macherla, Venkat and Hoffman, Thomas and Agarwal, Vinayak and Williams, Philip G and Dai, Jingqui and Neupane, Ram and Gurr, Joshua and Rodríguez, Andrés M C and Lamsa, Anne and Zhang, Chen and Dorrestein, Kathleen and Duggan, Brendan M and Almaliti, Jehad and Allard, Pierre-Marie and Phapale, Prasad and Nothias, Louis-Felix and Alexandrov, Theodore and Litaudon, Marc and Wolfender, Jean-Luc and Kyle, Jennifer E and Metz, Thomas O and Peryea, Tyler and Nguyen, Dac-Trung and VanLeer, Danielle and Shinn, Paul and Jadhav, Ajit and Müller, Rolf and Waters, Katrina M and Shi, Wenyuan and Liu, Xueting and Zhang, Lixin and Knight, Rob and Jensen, Paul R and Palsson, Bernhard Ø and Pogliano, Kit and Linington, Roger G and Gutiérrez, Marcelino and Lopes, Norberto P and Gerwick, William H and Moore, Bradley S and Dorrestein, Pieter C and Bandeira, Nuno (2016) Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 34 (8). pp. 828-837. ISSN 1087-0156 (https://doi.org/10.1038/nbt.3597)

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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.

ORCID iDs

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, Crüsemann, Max, Boudreau, Paul D, Esquenazi, Eduardo, Sandoval-Calderón, Mario, Kersten, Roland D, Pace, Laura A, Quinn, Robert A, Duncan, Katherine R ORCID logoORCID: https://orcid.org/0000-0002-3670-4849, 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, Jörn, 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, Rodríguez, Andrés M C, Lamsa, Anne, Zhang, Chen, Dorrestein, Kathleen, Duggan, Brendan M, Almaliti, Jehad, Allard, Pierre-Marie, Phapale, Prasad, Nothias, Louis-Felix, Alexandrov, Theodore, Litaudon, Marc, Wolfender, Jean-Luc, Kyle, Jennifer E, Metz, Thomas O, Peryea, Tyler, Nguyen, Dac-Trung, VanLeer, Danielle, Shinn, Paul, Jadhav, Ajit, Müller, Rolf, Waters, Katrina M, Shi, Wenyuan, Liu, Xueting, Zhang, Lixin, Knight, Rob, Jensen, Paul R, Palsson, Bernhard Ø, Pogliano, Kit, Linington, Roger G, Gutiérrez, Marcelino, Lopes, Norberto P, Gerwick, William H, Moore, Bradley S, Dorrestein, Pieter C and Bandeira, Nuno;
CORE (COnnecting REpositories)