An integrated targeted metabolomic platform for high-throughput metabolite profiling and automated data processing

Abstract

Multiple reaction monitoring (MRM)-based targeted metabolomics can simultaneously analyze up to hundreds of metabolites with high-throughput, good reproducibility, and wide dynamic range. However, when hundreds or thousands of MRM transitions are measured with tens to hundreds of biological samples, the complexity of MRM dataset acquired is no longer amenable to manual evaluation, and presents a challenge for targeted metabolomics. Here, we developed an R package, namely MRMAnalyzer, to process large set of MRM-based targeted metabolomics data automatically without any manual intervention. To demonstrate our MRMAnalyzer program, we first developed a targeted metabolomic method that simultaneously analyzes 182 metabolites in one 15-min LC run, and demonstrated the data processing procedures using MRMAnalyzer. The data processing steps include ''pseudo'' accurate m/z transformation, peak detection and alignment, metabolite identification, quality control check and statistical analysis. Finally, a targeted metabolomic assay was designed and integrated with MRMAnalyzer to profile the metabolic changes in Escherichia coli subjected to the protein expression. The generated MRM dataset consisting of more than 8000 MRM transitions were readily processed using MRMAnalyzer within 20 min without any manual intervention. Fourty seven out of 140 detected metabolites, enriched in six metabolic pathways, were found significantly affected in E. coli metabolome. In summary, a targeted metabolomic platform is developed for high-throughput metabolite profiling and automated data processing, and the MRMAnalyzer program is a high efficient informatics tool for large scale targeted metabolomics.

Overexpression of the histidine triad nucleotide‐binding protein 2 protects cardiac function in the adult mice after acute myocardial infarction

“…Subsequently, mass spectrum analysis was performed by the Agilent 6460 QqQ Analyzer (Agilent Technologies). The data were extracted using the MRM Analyzer as described previously . All the samples were mixed to determine their qualities and the relative standard deviation (lower than 30%) were considered reliable.…”

“…The data were extracted using the MRM Analyzer as described previously. 25 All the samples were mixed to determine their qualities and the relative standard deviation (lower than 30%) were considered reliable. The consumables and reagents used were as follows: the ACQUITY UPLC BEH Amide 1.7 μm × 2.1 mm × 100 mm column; acetonitrile (1499230-935, Merck); methyl alcohol (144 282,Merck); methanoic acid 06 450 (Fluka); ammonium acetate (70 221, Sigma-Aldrich); and all the 200 standards of candidate metabolites were purchased from Sigma-Aldrich.…”

Review of emerging metabolomic tools and resources: 2015–2016

“…MRMAnalyzer is an R package that allows for rapid processing of large set of multiple reaction monitoring (MRM) based targeted metabolomics data automatically without any manual intervention . Data processing steps include "pseduo" accurate mass‐to‐charge ( m/z ) transformation, peak detection and alignment, metabolite identification, quality control check, and statistical analyses.…”

AMP‐activated protein kinase activation in mediating phenylalanine‐induced neurotoxicity in experimental models of phenylketonuria

“…The levels of phenylalanine in mouse cerebral cortices were measured by multiple reaction monitoring (MRM)-based targeted metabolomic assay (Cai et al 2015). Cerebral cortices of the mice were rapidly excised and snap frozen in liquid nitrogen.…”