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Journal Articles Nature Biotechnology Year : 2016

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

Mingxun Wang (1) , Jeremy J. Carver (1) , Vanessa V. Phelan (2) , Laura M. Sanchez (2) , Neha Garg (2) , Yao Peng , Don Duy Nguyen (3) , Jeramie Watrous , Clifford A. Kapono , Tal Luzzatto-Knaan , Carla Porto , Amina Bouslimani , Alexey V. Melnik , Michael J. Meehan , Wei-Ting Liu (4) , Max Crüsemann , Paul D. Boudreau , Eduardo Esquenazi , Mario Sandoval-Calderon , Roland D. Kersten , Laura A. Pace , Robert A. Quinn , Katherine R. Duncan , Cheng-Chih Hsu , Dimitrios J. Floros , Ronnie G. Gavilan , Karin Keligrewe , Trent Northen , Rachel J. Dutton , Delphine Parrot (5) , Erin E. Carlson , Bertrand Aigle (6) , Charlotte F. Michelsen , Lars Jelsbak , Christian Sohlenkamp , Pavel Pevzner , Anna Edlund , Jeffrey Mclean , Jörn Piel (7) , Brian T. Murphy , Lena Gerwick , Chih-Chuang Liaw , Yu-Liang Yang (8) , Hans-Ulrich Humpf , Maria Maansson , Robert A. Keyzers , Amy C. Sims , Andrew R. Johnson , Ashley M. Sidebottom , Briand E. Sedio , Andreas Klitgaare , 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’neil , Enora Briand (9) , Eric J.N. Helfrich (7) , Eve A. Granotosky , 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 (10) , Samantha J. Mascuch , Sophie Tomasi (5) , Stefan Jenkins (11) , Venkat Macherla , Thomas Hoffman , Vinayak Agarwal , Philip G. Williams , Jingqui Dai , Ram Neupane , Joshua Gurr , Andrés M.C. Rodriguez , Anne Lamsa , Chen Zhang (12) , Kathleen Dorrestein , Brendan M. Duggan , Jehad Almaliti , Pierre-Marie Allard , Prasad Phapale , Louis-Felix Nothias , Theorodore Alexandrov , Marc Litaudon (13) , Jean-Luc Wolfender , Jennifer E. Kyle , Thomas O. Metz , Tyloer Peryea , Dac-Trung Nguyen (3) , Danielle Vanleer , Paul Shinn , Ajit Jadhav , Rolf Müller , Katrina M. Waters , Wenyuan Shi , Xueting Liu , Lixin Zhang (14) , Rob Knight , Paul R. Jensen (15) , Bernhard Ø Palsson , Kit Pogliano , Roger G. Linington , Marcelino Gutierrez , Norberto P. Lopes , William H. Gerwick (16) , Bradley S. Moore , Pieter C. Dorrestein (16) , Nuno Bandeira
Yao Peng
  • Function : Author
Jeramie Watrous
  • Function : Author
Clifford A. Kapono
  • Function : Author
Tal Luzzatto-Knaan
  • Function : Author
Carla Porto
  • Function : Author
Amina Bouslimani
  • Function : Author
Alexey V. Melnik
  • Function : Author
Michael J. Meehan
  • Function : Author
Max Crüsemann
  • Function : Author
Paul D. Boudreau
  • Function : Author
Eduardo Esquenazi
  • Function : Author
Mario Sandoval-Calderon
  • Function : Author
Roland D. Kersten
  • Function : Author
Laura A. Pace
  • Function : Author
Robert A. Quinn
  • Function : Author
Katherine R. Duncan
  • Function : Author
Cheng-Chih Hsu
  • Function : Author
Dimitrios J. Floros
  • Function : Author
Ronnie G. Gavilan
  • Function : Author
Karin Keligrewe
  • Function : Author
Trent Northen
  • Function : Author
Rachel J. Dutton
  • Function : Author
Erin E. Carlson
  • Function : Author
Charlotte F. Michelsen
  • Function : Author
Lars Jelsbak
  • Function : Author
Christian Sohlenkamp
  • Function : Author
Pavel Pevzner
  • Function : Author
Anna Edlund
  • Function : Author
Jeffrey Mclean
  • Function : Author
Brian T. Murphy
  • Function : Author
Lena Gerwick
  • Function : Author
Chih-Chuang Liaw
  • Function : Author
Hans-Ulrich Humpf
  • Function : Author
Maria Maansson
  • Function : Author
Robert A. Keyzers
  • Function : Author
Amy C. Sims
  • Function : Author
Andrew R. Johnson
  • Function : Author
Ashley M. Sidebottom
  • Function : Author
Briand E. Sedio
  • Function : Author
Andreas Klitgaare
  • Function : Author
Charles B. Larson
  • Function : Author
Cristopher A. Boya P.
  • Function : Author
Daniel Torres-Mendoza
  • Function : Author
David J. Gonzalez
  • Function : Author
Denise B. Silva
  • Function : Author
Lucas M. Marques
  • Function : Author
Daniel P. Demarque
  • Function : Author
Egle Pociute
  • Function : Author
Ellis C. O’neil
  • Function : Author
Eve A. Granotosky
  • Function : Author
Evgenia Glukhov
  • Function : Author
Florian Ryffel
  • Function : Author
Hailey Houson
  • Function : Author
Hosein Mohimani
  • Function : Author
Jenan J. Kharbush
  • Function : Author
Yi Zeng
Julia A. Vorholt
  • Function : Author
Kenji L. Kurita
  • Function : Author
Pep Charusanti
  • Function : Author
Kerry L. Mcphail
  • Function : Author
Kristian Fog Nielsen
  • Function : Author
Lisa Vuong
  • Function : Author
Maryam Elfeki
  • Function : Author
Matthew F. Traxler
  • Function : Author
Niclas Engene
  • Function : Author
Nobuhiro Koyama
  • Function : Author
Oliver B. Vining
  • Function : Author
Ralph Baric
  • Function : Author
Samantha J. Mascuch
  • Function : Author
Sophie Tomasi
Venkat Macherla
  • Function : Author
Thomas Hoffman
  • Function : Author
Vinayak Agarwal
  • Function : Author
Philip G. Williams
  • Function : Author
Jingqui Dai
  • Function : Author
Ram Neupane
  • Function : Author
Joshua Gurr
  • Function : Author
Andrés M.C. Rodriguez
  • Function : Author
Anne Lamsa
  • Function : Author
Kathleen Dorrestein
  • Function : Author
Brendan M. Duggan
  • Function : Author
Jehad Almaliti
  • Function : Author
Pierre-Marie Allard
Prasad Phapale
  • Function : Author
Louis-Felix Nothias
  • Function : Author
Theorodore Alexandrov
  • Function : Author
Marc Litaudon
Jean-Luc Wolfender
  • Function : Author
Jennifer E. Kyle
  • Function : Author
Thomas O. Metz
  • Function : Author
Tyloer Peryea
  • Function : Author
Danielle Vanleer
  • Function : Author
Paul Shinn
  • Function : Author
Ajit Jadhav
  • Function : Author
Rolf Müller
Katrina M. Waters
  • Function : Author
Wenyuan Shi
  • Function : Author
Xueting Liu
  • Function : Author
Rob Knight
Bernhard Ø Palsson
  • Function : Author
Kit Pogliano
  • Function : Author
Roger G. Linington
  • Function : Author
Marcelino Gutierrez
  • Function : Author
Norberto P. Lopes
  • Function : Author
Bradley S. Moore
  • Function : Author
Nuno Bandeira
  • Function : Author

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.

Dates and versions

hal-01371824 , version 1 (26-09-2016)

Identifiers

Cite

Mingxun Wang, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, et al.. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 2016, 34 (8), pp.828-837. ⟨10.1038/nbt.3597⟩. ⟨hal-01371824⟩
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