Improved experimental data processing for UHPLC–HRMS/MS lipidomics applied to nonalcoholic fatty liver disease

• Published in: Metabolomics 2017-11, Vol.13 (11), p.1, Article 142
• Main Authors: Patterson, R. E., Kirpich, A. S., Koelmel, J. P., Kalavalapalli, S., Morse, A. M., Cusi, K., Sunny, N. E., McIntyre, L. M., Garrett, T. J., Yost, R. A.
• Format: Article
• Language: English
• Subjects: Algorithms; Biochemistry; Biomedical and Life Sciences; Biomedicine; Cell Biology; Data acquisition; Data processing; Developmental Biology; Experimental data; Fatty liver; Filtration; Life Sciences; Liver; Liver diseases; Metabolomics; Molecular Medicine; Original Article; Quantitation; Rodents; Sample preparation; Standardization; Statistical analysis; Steatosis; Systematic errors; Triglycerides; Workflow
• ISSN: 1573-3882; 1573-3890
• DOI: 10.1007/s11306-017-1280-1

Introduction Untargeted metabolomics workflows include numerous points where variance and systematic errors can be introduced. Due to the diversity of the lipidome, manual peak picking and quantitation using molecule specific internal standards is unrealistic, and therefore quality peak picking algorithms and further feature processing and normalization algorithms are important. Subsequent normalization, data filtering, statistical analysis, and biological interpretation are simplified when quality data acquisition and feature processing are employed. Objectives Metrics for QC are important throughout the workflow. The robust workflow presented here provides techniques to ensure that QC checks are implemented throughout sample preparation, data acquisition, pre-processing, and analysis. Methods The untargeted lipidomics workflow includes sample standardization prior to acquisition, blocks of QC standards and blanks run at systematic intervals between randomized blocks of experimental data, blank feature filtering (BFF) to remove features not originating from the sample, and QC analysis of data acquisition and processing. Results The workflow was successfully applied to mouse liver samples, which were investigated to discern lipidomic changes throughout the development of nonalcoholic fatty liver disease (NAFLD). The workflow, including a novel filtering method, BFF, allows improved confidence in results and conclusions for lipidomic applications. Conclusion Using a mouse model developed for the study of the transition of NAFLD from an early stage known as simple steatosis, to the later stage, nonalcoholic steatohepatitis, in combination with our novel workflow, we have identified phosphatidylcholines, phosphatidylethanolamines, and triacylglycerols that may contribute to disease onset and/or progression.