GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

Daniel Petras; Vanessa V. Phelan; Deepa Acharya; Andrew E. Allen; Allegra T. Aron; Nuno Bandeira; Benjamin P. Bowen; Deirdre Belle-Oudry; Simon Boecker; Dale A. Cummings; Jessica M. Deutsch; Eoin Fahy; Neha Garg; Rachel Gregor; Jo Handelsman; Mirtha Navarro-Hoyos; Alan K. Jarmusch; Scott A. Jarmusch; Katherine Louie; Katherine N. Maloney; Michael T. Marty; Michael M. Meijler; Itzhak Mizrahi; Rachel L. Neve; Trent R. Northen; Carlos Molina-Santiago; Morgan Panitchpakdi; Benjamin Pullman; Aaron W. Puri; Robin Schmid; Shankar Subramaniam; Monica Thukral; Felipe Vasquez-Castro; Pieter C. Dorrestein; Mingxun Wang

doi:10.1038/s41592-021-01339-5

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

Daniel Petras
, Vanessa V. Phelan
, Deepa Acharya
, Andrew E. Allen
, Allegra T. Aron
, Nuno Bandeira
, Benjamin P. Bowen
, Deirdre Belle-Oudry
, Simon Boecker
, Dale A. Cummings
, Jessica M. Deutsch
, Eoin Fahy
, Neha Garg
, Rachel Gregor
, Jo Handelsman
, Mirtha Navarro-Hoyos
, Alan K. Jarmusch
, Scott A. Jarmusch
, Katherine Louie
, Katherine N. Maloney

Michael T. Marty, Michael M. Meijler, Itzhak Mizrahi, Rachel L. Neve, Trent R. Northen, Carlos Molina-Santiago, Morgan Panitchpakdi, Benjamin Pullman, Aaron W. Puri, Robin Schmid, Shankar Subramaniam, Monica Thukral, Felipe Vasquez-Castro, Pieter C. Dorrestein, Mingxun Wang

Chemistry & Biochemistry - Sci

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

65 Scopus citations

Original language	English (US)
Pages (from-to)	134-136
Number of pages	3
Journal	Nature Methods
Volume	19
Issue number	2
DOIs	https://doi.org/10.1038/s41592-021-01339-5
State	Published - Feb 2022

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

Access to Document

10.1038/s41592-021-01339-5

Cite this

Petras, D., Phelan, V. V., Acharya, D., Allen, A. E., Aron, A. T., Bandeira, N., Bowen, B. P., Belle-Oudry, D., Boecker, S., Cummings, D. A., Deutsch, J. M., Fahy, E., Garg, N., Gregor, R., Handelsman, J., Navarro-Hoyos, M., Jarmusch, A. K., Jarmusch, S. A., Louie, K., ... Wang, M. (2022). GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nature Methods, 19(2), 134-136. https://doi.org/10.1038/s41592-021-01339-5

Petras, D, Phelan, VV, Acharya, D, Allen, AE, Aron, AT, Bandeira, N, Bowen, BP, Belle-Oudry, D, Boecker, S, Cummings, DA, Deutsch, JM, Fahy, E, Garg, N, Gregor, R, Handelsman, J, Navarro-Hoyos, M, Jarmusch, AK, Jarmusch, SA, Louie, K, Maloney, KN, Marty, MT, Meijler, MM, Mizrahi, I, Neve, RL, Northen, TR, Molina-Santiago, C, Panitchpakdi, M, Pullman, B, Puri, AW, Schmid, R, Subramaniam, S, Thukral, M, Vasquez-Castro, F, Dorrestein, PC & Wang, M 2022, 'GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser', Nature Methods, vol. 19, no. 2, pp. 134-136. https://doi.org/10.1038/s41592-021-01339-5

@article{be76438d883a4143aa27db41b639a2a6,

title = "GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser",

author = "Daniel Petras and Phelan, \{Vanessa V.\} and Deepa Acharya and Allen, \{Andrew E.\} and Aron, \{Allegra T.\} and Nuno Bandeira and Bowen, \{Benjamin P.\} and Deirdre Belle-Oudry and Simon Boecker and Cummings, \{Dale A.\} and Deutsch, \{Jessica M.\} and Eoin Fahy and Neha Garg and Rachel Gregor and Jo Handelsman and Mirtha Navarro-Hoyos and Jarmusch, \{Alan K.\} and Jarmusch, \{Scott A.\} and Katherine Louie and Maloney, \{Katherine N.\} and Marty, \{Michael T.\} and Meijler, \{Michael M.\} and Itzhak Mizrahi and Neve, \{Rachel L.\} and Northen, \{Trent R.\} and Carlos Molina-Santiago and Morgan Panitchpakdi and Benjamin Pullman and Puri, \{Aaron W.\} and Robin Schmid and Shankar Subramaniam and Monica Thukral and Felipe Vasquez-Castro and Dorrestein, \{Pieter C.\} and Mingxun Wang",

note = "Funding Information: This work was, in part, supported by the National Institutes of Health (NIH) with grant numbers U19AG063744, U2CDK119886, OT2 OD030544, GM107550, R03CA211211, R24GM127667, 1R01LM013115 and P41GM103484, the National Science Foundation (NSF) with grants IOS-1656475 and ABI 1759980, and the Gordon and Betty Moore Foundation with grant GBMF7622. D.P. was supported by the Deutsche Forschungsgemeinschaft through the CMFI Cluster of Excellence (EXC 2124). V.V.P. was supported by NIH grant R35GM128690. N.B. and B.P. were supported by NIH grant P41-GM103484. M.T.M. was supported by NSF grant CHE-1845230. D.B. was supported by NSF grant DUE 16-25354. The I.M laboratory was supported by grants from the European Research Council (grant number 640384) and from the Israel Science Foundation (ISF number 1947/19). T.R.N., B.B. and K.L. were supported by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, which is supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. A.W.P. and D.A.C.J. were supported by NIH grant R00 GM 118762. This research was supported in part by the Intramural Research Program of the National Institute of Environmental Health Sciences of the NIH (ES103363-01). Furthermore, we would like to thank T. de Rond, L.-I. McCall, W. Bittremieux, K. Weldon and E. Gentry for testing the software and suggesting updates. We would like to thank V. Sharma, for working on the standalone MSView app during her Masters degree research 12 years ago, which provided some visualization inspiration for the GNPS Dashboard. We thank C. O{\textquoteright}Donovan and the team at MetaboLights for developing a well-documented API. Lastly, we thank all members of the research community who make their data publicly accessible, which contributes to open, transparent and reproducible science.",

year = "2022",

month = feb,

doi = "10.1038/s41592-021-01339-5",

language = "English (US)",

volume = "19",

pages = "134--136",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "2",

}

TY - JOUR

T1 - GNPS Dashboard

T2 - collaborative exploration of mass spectrometry data in the web browser

AU - Petras, Daniel

AU - Phelan, Vanessa V.

AU - Acharya, Deepa

AU - Allen, Andrew E.

AU - Aron, Allegra T.

AU - Bandeira, Nuno

AU - Bowen, Benjamin P.

AU - Belle-Oudry, Deirdre

AU - Boecker, Simon

AU - Cummings, Dale A.

AU - Deutsch, Jessica M.

AU - Fahy, Eoin

AU - Garg, Neha

AU - Gregor, Rachel

AU - Handelsman, Jo

AU - Navarro-Hoyos, Mirtha

AU - Jarmusch, Alan K.

AU - Jarmusch, Scott A.

AU - Louie, Katherine

AU - Maloney, Katherine N.

AU - Marty, Michael T.

AU - Meijler, Michael M.

AU - Mizrahi, Itzhak

AU - Neve, Rachel L.

AU - Northen, Trent R.

AU - Molina-Santiago, Carlos

AU - Panitchpakdi, Morgan

AU - Pullman, Benjamin

AU - Puri, Aaron W.

AU - Schmid, Robin

AU - Subramaniam, Shankar

AU - Thukral, Monica

AU - Vasquez-Castro, Felipe

AU - Dorrestein, Pieter C.

AU - Wang, Mingxun

N1 - Funding Information: This work was, in part, supported by the National Institutes of Health (NIH) with grant numbers U19AG063744, U2CDK119886, OT2 OD030544, GM107550, R03CA211211, R24GM127667, 1R01LM013115 and P41GM103484, the National Science Foundation (NSF) with grants IOS-1656475 and ABI 1759980, and the Gordon and Betty Moore Foundation with grant GBMF7622. D.P. was supported by the Deutsche Forschungsgemeinschaft through the CMFI Cluster of Excellence (EXC 2124). V.V.P. was supported by NIH grant R35GM128690. N.B. and B.P. were supported by NIH grant P41-GM103484. M.T.M. was supported by NSF grant CHE-1845230. D.B. was supported by NSF grant DUE 16-25354. The I.M laboratory was supported by grants from the European Research Council (grant number 640384) and from the Israel Science Foundation (ISF number 1947/19). T.R.N., B.B. and K.L. were supported by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, which is supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. A.W.P. and D.A.C.J. were supported by NIH grant R00 GM 118762. This research was supported in part by the Intramural Research Program of the National Institute of Environmental Health Sciences of the NIH (ES103363-01). Furthermore, we would like to thank T. de Rond, L.-I. McCall, W. Bittremieux, K. Weldon and E. Gentry for testing the software and suggesting updates. We would like to thank V. Sharma, for working on the standalone MSView app during her Masters degree research 12 years ago, which provided some visualization inspiration for the GNPS Dashboard. We thank C. O’Donovan and the team at MetaboLights for developing a well-documented API. Lastly, we thank all members of the research community who make their data publicly accessible, which contributes to open, transparent and reproducible science.

PY - 2022/2

Y1 - 2022/2

UR - https://www.scopus.com/pages/publications/85120680907

UR - https://www.scopus.com/pages/publications/85120680907#tab=citedBy

U2 - 10.1038/s41592-021-01339-5

DO - 10.1038/s41592-021-01339-5

M3 - Letter

C2 - 34862502

AN - SCOPUS:85120680907

SN - 1548-7091

VL - 19

SP - 134

EP - 136

JO - Nature Methods

JF - Nature Methods

IS - 2

ER -

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

ASJC Scopus subject areas

Access to Document

Other files and links

Cite this