title: MRM-DIFF: data processing strategy for differential analysis in large scale MRM-based lipidomics studies.
abstract: Based on theoretically calculated comprehensive lipid libraries, in lipidomics as many as 1000 multiple reaction monitoring (MRM) transitions can be monitored for each single run. On the other hand, lipid analysis from each MRM chromatogram requires tremendous manual efforts to identify and quantify lipid species. Isotopic peaks differing by up to a few atomic masses further complicate analysis. To accelerate the identification and quantification process we developed novel software, MRM-DIFF, for the differential analysis of large-scale MRM assays. It supports a correlation optimized warping (COW) algorithm to align MRM chromatograms and utilizes quality control (QC) sample datasets to automatically adjust the alignment parameters. Moreover, user-defined reference libraries that include the molecular formula, retention time, and MRM transition can be used to identify target lipids and to correct peak abundances by considering isotopic peaks. Here, we demonstrate the software pipeline and introduce key points for MRM-based lipidomics research to reduce the mis-identification and overestimation of lipid profiles. The MRM-DIFF program, example data set and the tutorials are downloadable at the "Standalone software" section of the PRIMe (Platform for RIKEN Metabolomics, http://prime.psc.riken.jp/) database website.
authors: Metabolome Informatics Research Team, Metabolomics Research Group, RIKEN Center for Sustainable Resource Science Yokohama, Japan ; Department of Biotechnology, Graduate School of Engineering, Osaka University Suita, Osaka, Japan.
authors: Hiroshi
authors: H
authors: Tsugawa
authors: Department of Biotechnology, Graduate School of Engineering, Osaka University Suita, Osaka, Japan.
authors: Erika
authors: E
authors: Ohta
authors: Department of Biotechnology, Graduate School of Engineering, Osaka University Suita, Osaka, Japan.
authors: Yoshihiro
authors: Y
authors: Izumi
authors: Reifycs Inc. Tokyo, Japan.
authors: Atsushi
authors: A
authors: Ogiwara
authors: Reifycs Inc. Tokyo, Japan.
authors: Daichi
authors: D
authors: Yukihira
authors: Department of Biotechnology, Graduate School of Engineering, Osaka University Suita, Osaka, Japan.
authors: Takeshi
authors: T
authors: Bamba
authors: Department of Biotechnology, Graduate School of Engineering, Osaka University Suita, Osaka, Japan.
authors: Eiichiro
authors: E
authors: Fukusaki
authors: Metabolome Informatics Research Team, Metabolomics Research Group, RIKEN Center for Sustainable Resource Science Yokohama, Japan ; National Institute of Genetics Shizuoka, Japan.
authors: Masanori
authors: M
authors: Arita
keywords: compound identification; differential analysis; isotopic peak estimation; lipidomics; multiple reaction monitoring