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

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

doi:10.1038/nbt.3597

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

Mingxun Wang, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen, Jeramie Watrous, Clifford A. Kapono, Tal Luzzatto-Knaan, Carla Porto, Amina Bouslimani, Alexey V. Melnik, Michael J. Meehan, Wei Ting Liu, Max Crüsemann, Paul D. Boudreau, Eduardo Esquenazi, Mario Sandoval-Calderón, Roland D. KerstenLaura A. Pace, Robert A. Quinn, Katherine R. Duncan, Cheng Chih Hsu, Dimitrios J. Floros, Ronnie G. Gavilan, Karin Kleigrewe, Trent Northen, Rachel J. Dutton, Delphine Parrot, Erin E. Carlson, Bertrand Aigle, Charlotte F. Michelsen, Lars Jelsbak, Christian Sohlenkamp, Pavel Pevzner, Anna Edlund, Jeffrey McLean, Jörn Piel, Brian T. Murphy, Lena Gerwick, Chih Chuang Liaw, Yu Liang Yang, Hans Ulrich Humpf, Maria Maansson, Robert A. Keyzers, Amy C. Sims, Andrew R. Johnson, Ashley M. Sidebottom, Brian E. Sedio, Andreas Klitgaard, Charles B. Larson, Cristopher A.P. Boya, Daniel Torres-Mendoza, David J. Gonzalez, Denise B. Silva, Lucas M. Marques, Daniel P. Demarque, Egle Pociute, Ellis C. O'Neill, Enora Briand, Eric J.N. Helfrich, Eve A. Granatosky, 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, Samantha J. Mascuch, Sophie Tomasi, Stefan Jenkins, Venkat Macherla, Thomas Hoffman, Vinayak Agarwal, Philip G. Williams, Jingqui Dai, Ram Neupane, Joshua Gurr, Andrés M.C. Rodríguez, Anne Lamsa, Chen Zhang, Kathleen Dorrestein, Brendan M. Duggan, Jehad Almaliti, Pierre Marie Allard, Prasad Phapale, Louis Felix Nothias, Theodore Alexandrov, Marc Litaudon, Jean Luc Wolfender, Jennifer E. Kyle, Thomas O. Metz, Tyler Peryea, Dac Trung Nguyen, Danielle VanLeer, Paul Shinn, Ajit Jadhav, Rolf Müller, Katrina M. Waters, Wenyuan Shi, Xueting Liu, Lixin Zhang, Rob Knight, Paul R. Jensen, Bernhard Palsson, Kit Pogliano, Roger G. Linington, Marcelino Gutiérrez, Norberto P. Lopes, William H. Gerwick, Bradley S. Moore, Pieter C. Dorrestein, Nuno Bandeira

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	828-837
Number of pages	10
Journal	Nature Biotechnology
Volume	34
Issue number	8
DOIs	https://doi.org/10.1038/nbt.3597
State	Published - 8 Sep 2016
Externally published	Yes

Bibliographical note

Funding Information:
This work was partially supported by US National Institutes of Health (NIH) grants 5P41GM103484-07, GM094802, AI095125, GM097509, S10RR029121, UL1RR031980, GM085770, U01TW0007401, and U01AI12316-01; N.B. was also partially supported as an Alfred P. Sloan Fellow. In addition, this work was supported by the National Institute of Allergy and Infectious Diseases (NIAID), NIH, and the Department of Health and Human Services, under Contract Number HHSN272200800060C. V.V.P. is supported by the NIH grant K01 GM103809. L.M.S. is supported by NIH IRACDA K12 GM068524 award. T.L.-K. is supported by the United States-Israel Binational Agricultural Research and Development Fund Vaadia-BARD No. FI-494-13. C.P. is supported by Science without Borders Program from CNPq. A.M.C.R. is supported by S?o Paulo Research Foundation (FAPESP) grant#2014/01651-8, 2012/18031-7. K.K. was supported by a fellowship within the Postdoc-Programme of the German Academic Exchange Service (DAAD). M.C. was supported by a Deutsche Forschungsgemeinschaft (D.F.G.) postdoctoral fellowship. E.B. is supported by a Marie Curie IOF Fellowship within the 7th European Community Framework Program (FP7-PEOPLE-2011-IOF, grant number 301244-CYANOMIC). C.-C.L. was supported by a grant from the Ministry of Science and Technology of Taiwan (MOST103-2628-B-110-001-MY3). P.C. and B.?.P. were supported by the Novo Nordisk Foundation. Lixin Zhang and Xueting Liu are supported by the National Program on Key Basic Research Project (2013BC734000) and the National Natural Science Foundation of China (81102369 and 31125002). D.P. is supported by an INSA grant, Rennes. R.R.S. is supported by FAPESP grant#2014/01884-2. D.P.D. is supported by FAPESP grant#2014/18052-0. L.M.M. is supported by FAPESP grant#2013/16496-5. D.B.S. is supported by FAPESP grant#2012/18031-7. N.P.L. is supported by FAPESP(2014/50265-3), CAPES/PNPD, CNPq-PQ 480 306385/2011-2, and CNPq-INCT-if. E.A.G. is supported by the Notre Dame Chemistry-Biochemistry-Biology Interface (CBBI) program and NIH T32 GM075762. W.S. and J.S.M. are supported by grants from the National Institutes of Health 1R01DE023810-01 and 1R01GM095373. A.E. is supported by a grant from the NIH K99DE024543. C.F.M. and L.J. are supported by the Villum Foundation VKR023113, the Augustinus Foundation 13-4656, and the Aase & Ejnar Danielsens Foundation 10-001120. M.S.-C. was supported by UC MEXUS-CONACYT Collaborative Grant CN-12-552. M.F.T. was supported by NIH grant 1F32GM089044. Contributions by B.E.S. were supported by NSF grant DEB 1010816 and a Smithsonian Institution Grand Challenges Award. E.J.N.H. and J.P. are supported by the DFG (Forschergruppe 854) and by SNF grant IZLSZ3-149025. K.F.N. and A.K. are supported by the Danish Council for Independent Research, Technology, and Production Sciences (09-064967) and the Agilent Thought Leader Program. A.C.S. and R.S.B. were supported by NIH/NIAID U19-AI106772. B.T.M. and M.E. were supported under Department of Defense grant #W81XWH-13-1-0171. Contributions by O.B.V. and K.L.M. were supported by Oregon Sea Grant NA10OAR4170059/R/BT-48, NIH 5R21AI085540, and U01TW006634-06. E.E.C., A.M.S., and A.R.J. were supported by an NSF CAREER Award, a Pew Biomedical Scholar Award (E.E.C.), a Sloan Research Fellow Award (E.E.C.), the Research Corporation for Science Advancement (Cottrell Scholar Award; E.E.C.) and an Indiana University Quantitative Chemical Biology trainee fellowship (A.R.J.). M.M. was supported by the Danish Research Council for Technology and Production Science with Sapere Aude (116262). P.-M.A. was supported by FNS for fellowship on Subside (200020-146200). We thank V. Paul, R. Taylor, L. Aluwihare, F. Rohwer, B. Pullman, J. Fang, M. Overgaard, M. Katze, R.D. Smith, S.K. Mazmanian, W. Fenical, E. Macagno, X. He, and C. Neubauer for feedback and support for their laboratory personnel to contribute to the work. We thank B. Gust and co-workers at the University of Tuebingen for assisting us to obtain Streptomyces sp. DSM5940.

Publisher Copyright:
© 2016 Nature America, Inc. All rights reserved.

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

Access to Document

10.1038/nbt.3597

Cite this

Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A. V., Meehan, M. J., Liu, W. T., Crüsemann, M., Boudreau, P. D., Esquenazi, E., Sandoval-Calderón, M., ... Bandeira, N. (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

@article{8506c716625541b9bff1d77c1a01c36c,

title = "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking",

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.",

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

note = "Funding Information: This work was partially supported by US National Institutes of Health (NIH) grants 5P41GM103484-07, GM094802, AI095125, GM097509, S10RR029121, UL1RR031980, GM085770, U01TW0007401, and U01AI12316-01; N.B. was also partially supported as an Alfred P. Sloan Fellow. In addition, this work was supported by the National Institute of Allergy and Infectious Diseases (NIAID), NIH, and the Department of Health and Human Services, under Contract Number HHSN272200800060C. V.V.P. is supported by the NIH grant K01 GM103809. L.M.S. is supported by NIH IRACDA K12 GM068524 award. T.L.-K. is supported by the United States-Israel Binational Agricultural Research and Development Fund Vaadia-BARD No. FI-494-13. C.P. is supported by Science without Borders Program from CNPq. A.M.C.R. is supported by S?o Paulo Research Foundation (FAPESP) grant#2014/01651-8, 2012/18031-7. K.K. was supported by a fellowship within the Postdoc-Programme of the German Academic Exchange Service (DAAD). M.C. was supported by a Deutsche Forschungsgemeinschaft (D.F.G.) postdoctoral fellowship. E.B. is supported by a Marie Curie IOF Fellowship within the 7th European Community Framework Program (FP7-PEOPLE-2011-IOF, grant number 301244-CYANOMIC). C.-C.L. was supported by a grant from the Ministry of Science and Technology of Taiwan (MOST103-2628-B-110-001-MY3). P.C. and B.?.P. were supported by the Novo Nordisk Foundation. Lixin Zhang and Xueting Liu are supported by the National Program on Key Basic Research Project (2013BC734000) and the National Natural Science Foundation of China (81102369 and 31125002). D.P. is supported by an INSA grant, Rennes. R.R.S. is supported by FAPESP grant#2014/01884-2. D.P.D. is supported by FAPESP grant#2014/18052-0. L.M.M. is supported by FAPESP grant#2013/16496-5. D.B.S. is supported by FAPESP grant#2012/18031-7. N.P.L. is supported by FAPESP(2014/50265-3), CAPES/PNPD, CNPq-PQ 480 306385/2011-2, and CNPq-INCT-if. E.A.G. is supported by the Notre Dame Chemistry-Biochemistry-Biology Interface (CBBI) program and NIH T32 GM075762. W.S. and J.S.M. are supported by grants from the National Institutes of Health 1R01DE023810-01 and 1R01GM095373. A.E. is supported by a grant from the NIH K99DE024543. C.F.M. and L.J. are supported by the Villum Foundation VKR023113, the Augustinus Foundation 13-4656, and the Aase & Ejnar Danielsens Foundation 10-001120. M.S.-C. was supported by UC MEXUS-CONACYT Collaborative Grant CN-12-552. M.F.T. was supported by NIH grant 1F32GM089044. Contributions by B.E.S. were supported by NSF grant DEB 1010816 and a Smithsonian Institution Grand Challenges Award. E.J.N.H. and J.P. are supported by the DFG (Forschergruppe 854) and by SNF grant IZLSZ3-149025. K.F.N. and A.K. are supported by the Danish Council for Independent Research, Technology, and Production Sciences (09-064967) and the Agilent Thought Leader Program. A.C.S. and R.S.B. were supported by NIH/NIAID U19-AI106772. B.T.M. and M.E. were supported under Department of Defense grant #W81XWH-13-1-0171. Contributions by O.B.V. and K.L.M. were supported by Oregon Sea Grant NA10OAR4170059/R/BT-48, NIH 5R21AI085540, and U01TW006634-06. E.E.C., A.M.S., and A.R.J. were supported by an NSF CAREER Award, a Pew Biomedical Scholar Award (E.E.C.), a Sloan Research Fellow Award (E.E.C.), the Research Corporation for Science Advancement (Cottrell Scholar Award; E.E.C.) and an Indiana University Quantitative Chemical Biology trainee fellowship (A.R.J.). M.M. was supported by the Danish Research Council for Technology and Production Science with Sapere Aude (116262). P.-M.A. was supported by FNS for fellowship on Subside (200020-146200). We thank V. Paul, R. Taylor, L. Aluwihare, F. Rohwer, B. Pullman, J. Fang, M. Overgaard, M. Katze, R.D. Smith, S.K. Mazmanian, W. Fenical, E. Macagno, X. He, and C. Neubauer for feedback and support for their laboratory personnel to contribute to the work. We thank B. Gust and co-workers at the University of Tuebingen for assisting us to obtain Streptomyces sp. DSM5940. Publisher Copyright: {\textcopyright} 2016 Nature America, Inc. All rights reserved.",

year = "2016",

month = sep,

day = "8",

doi = "10.1038/nbt.3597",

language = "English",

volume = "34",

pages = "828--837",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

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Wang, M, Carver, JJ, Phelan, VV, Sanchez, LM, Garg, N, Peng, Y, Nguyen, DD, Watrous, J, Kapono, CA, Luzzatto-Knaan, T, Porto, C, Bouslimani, A, Melnik, AV, Meehan, MJ, Liu, WT, Crüsemann, M, Boudreau, PD, Esquenazi, E, Sandoval-Calderón, M, Kersten, RD, Pace, LA, Quinn, RA, Duncan, KR, Hsu, CC, Floros, DJ, Gavilan, RG, Kleigrewe, K, Northen, T, Dutton, RJ, Parrot, D, Carlson, EE, Aigle, B, Michelsen, CF, Jelsbak, L, Sohlenkamp, C, Pevzner, P, Edlund, A, McLean, J, Piel, J, Murphy, BT, Gerwick, L, Liaw, CC, Yang, YL, Humpf, HU, Maansson, M, Keyzers, RA, Sims, AC, Johnson, AR, Sidebottom, AM, Sedio, BE, Klitgaard, A, Larson, CB, Boya, CAP, Torres-Mendoza, D, Gonzalez, DJ, Silva, DB, Marques, LM, Demarque, DP, Pociute, E, O'Neill, EC, Briand, E, Helfrich, EJN, Granatosky, EA, Glukhov, E, Ryffel, F, Houson, H, Mohimani, H, Kharbush, JJ, Zeng, Y, Vorholt, JA, Kurita, KL, Charusanti, P, McPhail, KL, Nielsen, KF, Vuong, L, Elfeki, M, Traxler, MF, Engene, N, Koyama, N, Vining, OB, Baric, R, Silva, RR, Mascuch, SJ, Tomasi, S, Jenkins, S, Macherla, V, Hoffman, T, Agarwal, V, Williams, PG, Dai, J, Neupane, R, Gurr, J, Rodríguez, AMC, Lamsa, A, Zhang, C, Dorrestein, K, Duggan, BM, Almaliti, J, Allard, PM, Phapale, P, Nothias, LF, Alexandrov, T, Litaudon, M, Wolfender, JL, Kyle, JE, Metz, TO, Peryea, T, Nguyen, DT, VanLeer, D, Shinn, P, Jadhav, A, Müller, R, Waters, KM, Shi, W, Liu, X, Zhang, L, Knight, R, Jensen, PR, Palsson, B, Pogliano, K, Linington, RG, Gutiérrez, M, Lopes, NP, Gerwick, WH, Moore, BS, Dorrestein, PC & Bandeira, N 2016, 'Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking', Nature Biotechnology, vol. 34, no. 8, pp. 828-837. https://doi.org/10.1038/nbt.3597

TY - JOUR

T1 - Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

AU - Wang, Mingxun

AU - Carver, Jeremy J.

AU - Phelan, Vanessa V.

AU - Sanchez, Laura M.

AU - Garg, Neha

AU - Peng, Yao

AU - Nguyen, Don Duy

AU - Watrous, Jeramie

AU - Kapono, Clifford A.

AU - Luzzatto-Knaan, Tal

AU - Porto, Carla

AU - Bouslimani, Amina

AU - Melnik, Alexey V.

AU - Meehan, Michael J.

AU - Liu, Wei Ting

AU - Crüsemann, Max

AU - Boudreau, Paul D.

AU - Esquenazi, Eduardo

AU - Sandoval-Calderón, Mario

AU - Kersten, Roland D.

AU - Pace, Laura A.

AU - Quinn, Robert A.

AU - Duncan, Katherine R.

AU - Hsu, Cheng Chih

AU - Floros, Dimitrios J.

AU - Gavilan, Ronnie G.

AU - Kleigrewe, Karin

AU - Northen, Trent

AU - Dutton, Rachel J.

AU - Parrot, Delphine

AU - Carlson, Erin E.

AU - Aigle, Bertrand

AU - Michelsen, Charlotte F.

AU - Jelsbak, Lars

AU - Sohlenkamp, Christian

AU - Pevzner, Pavel

AU - Edlund, Anna

AU - McLean, Jeffrey

AU - Piel, Jörn

AU - Murphy, Brian T.

AU - Gerwick, Lena

AU - Liaw, Chih Chuang

AU - Yang, Yu Liang

AU - Humpf, Hans Ulrich

AU - Maansson, Maria

AU - Keyzers, Robert A.

AU - Sims, Amy C.

AU - Johnson, Andrew R.

AU - Sidebottom, Ashley M.

AU - Sedio, Brian E.

AU - Klitgaard, Andreas

AU - Larson, Charles B.

AU - Boya, Cristopher A.P.

AU - Torres-Mendoza, Daniel

AU - Gonzalez, David J.

AU - Silva, Denise B.

AU - Marques, Lucas M.

AU - Demarque, Daniel P.

AU - Pociute, Egle

AU - O'Neill, Ellis C.

AU - Briand, Enora

AU - Helfrich, Eric J.N.

AU - Granatosky, Eve A.

AU - Glukhov, Evgenia

AU - Ryffel, Florian

AU - Houson, Hailey

AU - Mohimani, Hosein

AU - Kharbush, Jenan J.

AU - Zeng, Yi

AU - Vorholt, Julia A.

AU - Kurita, Kenji L.

AU - Charusanti, Pep

AU - McPhail, Kerry L.

AU - Nielsen, Kristian Fog

AU - Vuong, Lisa

AU - Elfeki, Maryam

AU - Traxler, Matthew F.

AU - Engene, Niclas

AU - Koyama, Nobuhiro

AU - Vining, Oliver B.

AU - Baric, Ralph

AU - Silva, Ricardo R.

AU - Mascuch, Samantha J.

AU - Tomasi, Sophie

AU - Jenkins, Stefan

AU - Macherla, Venkat

AU - Hoffman, Thomas

AU - Agarwal, Vinayak

AU - Williams, Philip G.

AU - Dai, Jingqui

AU - Neupane, Ram

AU - Gurr, Joshua

AU - Rodríguez, Andrés M.C.

AU - Lamsa, Anne

AU - Zhang, Chen

AU - Dorrestein, Kathleen

AU - Duggan, Brendan M.

AU - Almaliti, Jehad

AU - Allard, Pierre Marie

AU - Phapale, Prasad

AU - Nothias, Louis Felix

AU - Alexandrov, Theodore

AU - Litaudon, Marc

AU - Wolfender, Jean Luc

AU - Kyle, Jennifer E.

AU - Metz, Thomas O.

AU - Peryea, Tyler

AU - Nguyen, Dac Trung

AU - VanLeer, Danielle

AU - Shinn, Paul

AU - Jadhav, Ajit

AU - Müller, Rolf

AU - Waters, Katrina M.

AU - Shi, Wenyuan

AU - Liu, Xueting

AU - Zhang, Lixin

AU - Knight, Rob

AU - Jensen, Paul R.

AU - Palsson, Bernhard

AU - Pogliano, Kit

AU - Linington, Roger G.

AU - Gutiérrez, Marcelino

AU - Lopes, Norberto P.

AU - Gerwick, William H.

AU - Moore, Bradley S.

AU - Dorrestein, Pieter C.

AU - Bandeira, Nuno

N1 - Funding Information: This work was partially supported by US National Institutes of Health (NIH) grants 5P41GM103484-07, GM094802, AI095125, GM097509, S10RR029121, UL1RR031980, GM085770, U01TW0007401, and U01AI12316-01; N.B. was also partially supported as an Alfred P. Sloan Fellow. In addition, this work was supported by the National Institute of Allergy and Infectious Diseases (NIAID), NIH, and the Department of Health and Human Services, under Contract Number HHSN272200800060C. V.V.P. is supported by the NIH grant K01 GM103809. L.M.S. is supported by NIH IRACDA K12 GM068524 award. T.L.-K. is supported by the United States-Israel Binational Agricultural Research and Development Fund Vaadia-BARD No. FI-494-13. C.P. is supported by Science without Borders Program from CNPq. A.M.C.R. is supported by S?o Paulo Research Foundation (FAPESP) grant#2014/01651-8, 2012/18031-7. K.K. was supported by a fellowship within the Postdoc-Programme of the German Academic Exchange Service (DAAD). M.C. was supported by a Deutsche Forschungsgemeinschaft (D.F.G.) postdoctoral fellowship. E.B. is supported by a Marie Curie IOF Fellowship within the 7th European Community Framework Program (FP7-PEOPLE-2011-IOF, grant number 301244-CYANOMIC). C.-C.L. was supported by a grant from the Ministry of Science and Technology of Taiwan (MOST103-2628-B-110-001-MY3). P.C. and B.?.P. were supported by the Novo Nordisk Foundation. Lixin Zhang and Xueting Liu are supported by the National Program on Key Basic Research Project (2013BC734000) and the National Natural Science Foundation of China (81102369 and 31125002). D.P. is supported by an INSA grant, Rennes. R.R.S. is supported by FAPESP grant#2014/01884-2. D.P.D. is supported by FAPESP grant#2014/18052-0. L.M.M. is supported by FAPESP grant#2013/16496-5. D.B.S. is supported by FAPESP grant#2012/18031-7. N.P.L. is supported by FAPESP(2014/50265-3), CAPES/PNPD, CNPq-PQ 480 306385/2011-2, and CNPq-INCT-if. E.A.G. is supported by the Notre Dame Chemistry-Biochemistry-Biology Interface (CBBI) program and NIH T32 GM075762. W.S. and J.S.M. are supported by grants from the National Institutes of Health 1R01DE023810-01 and 1R01GM095373. A.E. is supported by a grant from the NIH K99DE024543. C.F.M. and L.J. are supported by the Villum Foundation VKR023113, the Augustinus Foundation 13-4656, and the Aase & Ejnar Danielsens Foundation 10-001120. M.S.-C. was supported by UC MEXUS-CONACYT Collaborative Grant CN-12-552. M.F.T. was supported by NIH grant 1F32GM089044. Contributions by B.E.S. were supported by NSF grant DEB 1010816 and a Smithsonian Institution Grand Challenges Award. E.J.N.H. and J.P. are supported by the DFG (Forschergruppe 854) and by SNF grant IZLSZ3-149025. K.F.N. and A.K. are supported by the Danish Council for Independent Research, Technology, and Production Sciences (09-064967) and the Agilent Thought Leader Program. A.C.S. and R.S.B. were supported by NIH/NIAID U19-AI106772. B.T.M. and M.E. were supported under Department of Defense grant #W81XWH-13-1-0171. Contributions by O.B.V. and K.L.M. were supported by Oregon Sea Grant NA10OAR4170059/R/BT-48, NIH 5R21AI085540, and U01TW006634-06. E.E.C., A.M.S., and A.R.J. were supported by an NSF CAREER Award, a Pew Biomedical Scholar Award (E.E.C.), a Sloan Research Fellow Award (E.E.C.), the Research Corporation for Science Advancement (Cottrell Scholar Award; E.E.C.) and an Indiana University Quantitative Chemical Biology trainee fellowship (A.R.J.). M.M. was supported by the Danish Research Council for Technology and Production Science with Sapere Aude (116262). P.-M.A. was supported by FNS for fellowship on Subside (200020-146200). We thank V. Paul, R. Taylor, L. Aluwihare, F. Rohwer, B. Pullman, J. Fang, M. Overgaard, M. Katze, R.D. Smith, S.K. Mazmanian, W. Fenical, E. Macagno, X. He, and C. Neubauer for feedback and support for their laboratory personnel to contribute to the work. We thank B. Gust and co-workers at the University of Tuebingen for assisting us to obtain Streptomyces sp. DSM5940. Publisher Copyright: © 2016 Nature America, Inc. All rights reserved.

PY - 2016/9/8

Y1 - 2016/9/8

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84981297901&partnerID=8YFLogxK

U2 - 10.1038/nbt.3597

DO - 10.1038/nbt.3597

M3 - Article

C2 - 27504778

AN - SCOPUS:84981297901

SN - 1087-0156

VL - 34

SP - 828

EP - 837

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 8

ER -

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

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