Computational protocol: Apolipoprotein E4 and Insulin Resistance Interact to Impair Cognition and Alter the Epigenome and Metabolome

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Protocol publication

[…] Hippocampi were dissected and homogenized in RIPA (500 μl). Metabolites were extracted from 100 μl of hippocampal homogenate and untargeted metabolomics was completed as described. Metabolomics data was processed using MarkerView and Peakview software (AB SCIEX) and Metaboanalyst. Metabolite identification was based on mass error (<30 ppm) and MS/MS fragment ions. Many metabolites were further confirmed using retention time and comparison to authentic standards ( ± 1 min) from an in-house library (IROA Technologies). LipidMaps, METLIN and HMDB databases were used for MS and MS/MS matching. Metaboanalyst heatmap and pathway analyses were performed as described. For integrated pathway analyses, the parameters were set to ‘global test’ and ‘relative betweenness centrality’. […]

Pipeline specifications

Software tools MarkerView, MetaboAnalyst
Databases HMDB METLIN
Application MS-based untargeted metabolomics
Organisms Mus musculus
Diseases Alzheimer Disease, Dementia, Diabetes Mellitus, Metabolic Diseases, Neoplasms, Adipose Tissue
Chemicals Pentosephosphates, Purines, Glutamic Acid