flippant–An R package for the automated analysis of fluorescence-based scramblase assays

BMC Bioinformatics

Software

Birgit Ploier¹  Anant K. Menon¹  Michael A. Goren¹  Richard J. Cotton²  Johannes Graumann³ 

[1] Department of Biochemistry, Weill Cornell Medical College, 10065, New York, NY, USA;Research Division, Weill Cornell Medicine–Qatar, P.O.Box 24144, Doha, State of Qatar;Research Division, Weill Cornell Medicine–Qatar, P.O.Box 24144, Doha, State of Qatar;Current Address: Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, D-61231, Bad Nauheim, Germany;

关键词: Scramblase;    Dithionite scramblase assay;    R;   

DOI  :  10.1186/s12859-017-1542-y

 received in 2016-09-12, accepted in 2017-02-08,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe lipid scrambling activity of protein extracts and purified scramblases is typically measured using a fluorescence-based assay. While the assay has yielded insight into the scramblase activity in crude membrane preparations, functional validation of candidate scramblases, stoichiometry of scramblase complexes as well as ATP-dependence of flippases, data analysis in its context has remained a task involving many manual steps.ResultsWith the extension package “flippant” to R, a free software environment for statistical computing and graphics, we introduce an integrated solution for the analysis and publication-grade graphical presentation of dithionite scramblase assays and demonstrate its utility in revisiting an originally manual analysis from the publication record, closely reproducing the reported results.Conclusions“flippant” allows for quick, reproducible data analysis of scramblase activity assays and provides a platform for review, dissemination and extension of the strategies it employs.

【 授权许可】

CC BY   
© The Author(s). 2017