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 & 107 others 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 Boya P, 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 Ø 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 journalArticle

386 Citations (Scopus)

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.

LanguageEnglish
Pages828-37
Number of pages10
JournalNature Biotechnology
Volume34
Issue number8
DOIs
Publication statusPublished - 9 Aug 2016

Fingerprint

Social Networking
Biological Products
Mass spectrometry
Mass Spectrometry
Biotechnology
Knowledge Bases
Information Dissemination
Spectrometry
Medicine
Tandem Mass Spectrometry
Throughput
Libraries
Spectrum Analysis
Natural products
Networking
Databases

Keywords

  • mass spectroscopy
  • computational platforms
  • natural products
  • databases
  • data sharing
  • data curation
  • open-access knowledge base
  • social networking

Cite this

Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., ... Bandeira, N. (2016). Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 34(8), 828-37. https://doi.org/10.1038/nbt.3597
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 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 ; Bandeira, Nuno. / Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. In: Nature Biotechnology. 2016 ; Vol. 34, No. 8. pp. 828-37.
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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, W-T, Crüsemann, M, Boudreau, PD, Esquenazi, E, Sandoval-Calderón, M, Kersten, RD, Pace, LA, Quinn, RA, Duncan, KR, Hsu, C-C, 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, C-C, Yang, Y-L, Humpf, H-U, Maansson, M, Keyzers, RA, Sims, AC, Johnson, AR, Sidebottom, AM, Sedio, BE, Klitgaard, A, Larson, CB, Boya P, CA, 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, P-M, Phapale, P, Nothias, L-F, Alexandrov, T, Litaudon, M, Wolfender, J-L, Kyle, JE, Metz, TO, Peryea, T, Nguyen, D-T, VanLeer, D, Shinn, P, Jadhav, A, Müller, R, Waters, KM, Shi, W, Liu, X, Zhang, L, Knight, R, Jensen, PR, Palsson, BØ, 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. 828-37. https://doi.org/10.1038/nbt.3597

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 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; Bandeira, Nuno.

In: Nature Biotechnology, Vol. 34, No. 8, 09.08.2016, p. 828-37.

Research output: Contribution to journalArticle

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 P, Cristopher A

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 Ø

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

PY - 2016/8/9

Y1 - 2016/8/9

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.

KW - mass spectroscopy

KW - computational platforms

KW - natural products

KW - databases

KW - data sharing

KW - data curation

KW - open-access knowledge base

KW - social networking

UR - http://www.nature.com/nbt/index.html

U2 - 10.1038/nbt.3597

DO - 10.1038/nbt.3597

M3 - Article

VL - 34

SP - 828

EP - 837

JO - Nature Biotechnology

T2 - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 8

ER -