Guiding the choice of informatics software and tools for lipidomics research applications

Ni, Zhixu; Wolk, Michele; Jukes, Geoff; Espinosa, Karla Mendivelso; Ahrends, Robert; Aimo, Lucila; Alvarez-Jarreta, Jorge; Andrews, Simon; Andrews, Robert; Bridge, Alan; Clair, Geremy C.; Conroy, Matthew J.; Fahy, Eoin; Gaud, Caroline; Goracci, Laura; Hartler, Juergen; Hoffmann, Nils; Kopczyinki, Dominik; Korf, Ansgar; Lopez-Clavijo, Andrea F.; Malik, Adnan; Ackerman, Jacobo Miranda; Molenaar, Martijn R.; O'Donovan, Claire; Pluskal, Tomas; Shevchenko, Andrej; Slenter, Denise; Siuzdak, Gary; Kutmon, Martina; Tsugawa, Hiroshi; Willighagen, Egon L.; Xia, Jianguo; O'Donnell, Valerie B.; Fedorova, Maria

Guiding the choice of informatics software and tools for lipidomics research applications

Ni Z, Wolk M, Jukes G, Espinosa KM, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, et al. (2022)
Nature Methods .

Zeitschriftenaufsatz | E-Veröff. vor dem Druck | Englisch

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DOI

https://doi.org/10.1038/s41592-022-01710-0

Autor*in

Ni, Zhixu; Wolk, Michele; Jukes, Geoff; Espinosa, Karla Mendivelso; Ahrends, Robert; Aimo, Lucila; Alvarez-Jarreta, Jorge; Andrews, Simon; Andrews, Robert; Bridge, Alan; Clair, Geremy C.; Conroy, Matthew J.
Alle

Einrichtung

Centrum für Biotechnologie

Abstract / Bemerkung

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

Erscheinungsjahr

2022

Zeitschriftentitel

Nature Methods

ISSN

1548-7091

eISSN

1548-7105

Page URI

https://pub.uni-bielefeld.de/record/2968524

Zitieren

Ni Z, Wolk M, Jukes G, et al. Guiding the choice of informatics software and tools for lipidomics research applications. Nature Methods . 2022.

Ni, Z., Wolk, M., Jukes, G., Espinosa, K. M., Ahrends, R., Aimo, L., Alvarez-Jarreta, J., et al. (2022). Guiding the choice of informatics software and tools for lipidomics research applications. Nature Methods . https://doi.org/10.1038/s41592-022-01710-0

Ni, Zhixu, Wolk, Michele, Jukes, Geoff, Espinosa, Karla Mendivelso, Ahrends, Robert, Aimo, Lucila, Alvarez-Jarreta, Jorge, et al. 2022. “Guiding the choice of informatics software and tools for lipidomics research applications”. Nature Methods .

Ni, Z., Wolk, M., Jukes, G., Espinosa, K. M., Ahrends, R., Aimo, L., Alvarez-Jarreta, J., Andrews, S., Andrews, R., Bridge, A., et al. (2022). Guiding the choice of informatics software and tools for lipidomics research applications. Nature Methods .

Ni, Z., et al., 2022. Guiding the choice of informatics software and tools for lipidomics research applications. Nature Methods .

Z. Ni, et al., “Guiding the choice of informatics software and tools for lipidomics research applications”, Nature Methods , 2022.

Ni, Z., Wolk, M., Jukes, G., Espinosa, K.M., Ahrends, R., Aimo, L., Alvarez-Jarreta, J., Andrews, S., Andrews, R., Bridge, A., Clair, G.C., Conroy, M.J., Fahy, E., Gaud, C., Goracci, L., Hartler, J., Hoffmann, N., Kopczyinki, D., Korf, A., Lopez-Clavijo, A.F., Malik, A., Ackerman, J.M., Molenaar, M.R., O'Donovan, C., Pluskal, T., Shevchenko, A., Slenter, D., Siuzdak, G., Kutmon, M., Tsugawa, H., Willighagen, E.L., Xia, J., O'Donnell, V.B., Fedorova, M.: Guiding the choice of informatics software and tools for lipidomics research applications. Nature Methods . (2022).

Ni, Zhixu, Wolk, Michele, Jukes, Geoff, Espinosa, Karla Mendivelso, Ahrends, Robert, Aimo, Lucila, Alvarez-Jarreta, Jorge, Andrews, Simon, Andrews, Robert, Bridge, Alan, Clair, Geremy C., Conroy, Matthew J., Fahy, Eoin, Gaud, Caroline, Goracci, Laura, Hartler, Juergen, Hoffmann, Nils, Kopczyinki, Dominik, Korf, Ansgar, Lopez-Clavijo, Andrea F., Malik, Adnan, Ackerman, Jacobo Miranda, Molenaar, Martijn R., O'Donovan, Claire, Pluskal, Tomas, Shevchenko, Andrej, Slenter, Denise, Siuzdak, Gary, Kutmon, Martina, Tsugawa, Hiroshi, Willighagen, Egon L., Xia, Jianguo, O'Donnell, Valerie B., and Fedorova, Maria. “Guiding the choice of informatics software and tools for lipidomics research applications”. Nature Methods (2022).

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