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 (US) |
|---|---|
| Pages (from-to) | 828-837 |
| Number of pages | 10 |
| Journal | Nature biotechnology |
| Volume | 34 |
| Issue number | 8 |
| DOIs | |
| State | Published - Sep 8 2016 |
| Externally published | Yes |
ASJC Scopus subject areas
- Biotechnology
- Bioengineering
- Applied Microbiology and Biotechnology
- Molecular Medicine
- Biomedical Engineering
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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. / 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.; 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, Cristopher A.P.; 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; Pogliano, Kit; Linington, Roger G.; Gutiérrez, Marcelino; Lopes, Norberto P.; Gerwick, William H.; Moore, Bradley S.; Dorrestein, Pieter C.; Bandeira, Nuno.
In: Nature biotechnology, Vol. 34, No. 8, 08.09.2016, p. 828-837.Research output: Contribution to journal › Review article › peer-review
}
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
UR - http://www.scopus.com/inward/citedby.url?scp=84981297901&partnerID=8YFLogxK
U2 - 10.1038/nbt.3597
DO - 10.1038/nbt.3597
M3 - Review article
C2 - 27504778
AN - SCOPUS:84981297901
VL - 34
SP - 828
EP - 837
JO - Biotechnology
JF - Biotechnology
SN - 1087-0156
IS - 8
ER -