LipidCreator workbench to probe the lipidomic landscape

Bing Peng; Dominik Kopczynski; Brian S. Pratt; Christer S. Ejsing; Bo Burla; Martin Hermansson; Peter Imre Benke; Sock Hwee Tan; Mark Y. Chan; Federico Torta; Dominik Schwudke; Sven W. Meckelmann; Cristina Coman; Oliver J. Schmitz; Brendan MacLean; Mailin Christin Manke; Oliver Borst; Markus R. Wenk; Nils Hoffmann; Robert Ahrends

doi:10.1038/s41467-020-15960-z

LipidCreator workbench to probe the lipidomic landscape

Bing Peng, Dominik Kopczynski, Brian S. Pratt, Christer S. Ejsing, Bo Burla, Martin Hermansson, Peter Imre Benke, Sock Hwee Tan, Mark Y. Chan, Federico Torta, Dominik Schwudke, Sven W. Meckelmann, Cristina Coman, Oliver J. Schmitz, Brendan MacLean, Mailin Christin Manke, Oliver Borst, Markus R. Wenk, Nils Hoffmann, Robert Ahrends^*

^*Corresponding author for this work

Department of Biochemistry and Molecular Biology

Research output: Contribution to journal › Journal article › Research › peer-review

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Abstract

Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.

Original language	English
Article number	2057
Journal	Nature Communications
Volume	11
ISSN	2041-1723
DOIs	https://doi.org/10.1038/s41467-020-15960-z
Publication status	Published - 2020

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10.1038/s41467-020-15960-zLicence: CC BY

Open Access VersionFinal published version, 3.67 MBLicence: CC BY

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Peng, B., Kopczynski, D., Pratt, B. S., Ejsing, C. S., Burla, B., Hermansson, M., Benke, P. I., Tan, S. H., Chan, M. Y., Torta, F., Schwudke, D., Meckelmann, S. W., Coman, C., Schmitz, O. J., MacLean, B., Manke, M. C., Borst, O., Wenk, M. R., Hoffmann, N., & Ahrends, R. (2020). LipidCreator workbench to probe the lipidomic landscape. Nature Communications, 11, Article 2057. https://doi.org/10.1038/s41467-020-15960-z

@article{40fdf9e668ec4fb6872cbaf6c831f637,

title = "LipidCreator workbench to probe the lipidomic landscape",

abstract = "Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.",

author = "Bing Peng and Dominik Kopczynski and Pratt, {Brian S.} and Ejsing, {Christer S.} and Bo Burla and Martin Hermansson and Benke, {Peter Imre} and Tan, {Sock Hwee} and Chan, {Mark Y.} and Federico Torta and Dominik Schwudke and Meckelmann, {Sven W.} and Cristina Coman and Schmitz, {Oliver J.} and Brendan MacLean and Manke, {Mailin Christin} and Oliver Borst and Wenk, {Markus R.} and Nils Hoffmann and Robert Ahrends",

year = "2020",

doi = "10.1038/s41467-020-15960-z",

language = "English",

volume = "11",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

}

Peng, B, Kopczynski, D, Pratt, BS, Ejsing, CS, Burla, B, Hermansson, M, Benke, PI, Tan, SH, Chan, MY, Torta, F, Schwudke, D, Meckelmann, SW, Coman, C, Schmitz, OJ, MacLean, B, Manke, MC, Borst, O, Wenk, MR, Hoffmann, N & Ahrends, R 2020, 'LipidCreator workbench to probe the lipidomic landscape', Nature Communications, vol. 11, 2057. https://doi.org/10.1038/s41467-020-15960-z

TY - JOUR

T1 - LipidCreator workbench to probe the lipidomic landscape

AU - Peng, Bing

AU - Kopczynski, Dominik

AU - Pratt, Brian S.

AU - Ejsing, Christer S.

AU - Burla, Bo

AU - Hermansson, Martin

AU - Benke, Peter Imre

AU - Tan, Sock Hwee

AU - Chan, Mark Y.

AU - Torta, Federico

AU - Schwudke, Dominik

AU - Meckelmann, Sven W.

AU - Coman, Cristina

AU - Schmitz, Oliver J.

AU - MacLean, Brendan

AU - Manke, Mailin Christin

AU - Borst, Oliver

AU - Wenk, Markus R.

AU - Hoffmann, Nils

AU - Ahrends, Robert

PY - 2020

Y1 - 2020

N2 - Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.

AB - Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.

U2 - 10.1038/s41467-020-15960-z

DO - 10.1038/s41467-020-15960-z

M3 - Journal article

C2 - 32345972

AN - SCOPUS:85083958409

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

M1 - 2057

ER -

LipidCreator workbench to probe the lipidomic landscape

Abstract

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