The AMBITION study

Assessing Mitochondrial BIoenergetics in stable coronary artery disease: A Translational study Integrating multiOmic analysis of human left ventricular tissue and quaNtitative stress perfusion cardiovascular magnetic resonance

The notebook contains: Metabolomics data of patients myocardial biopsies that were analysed by liquid chromatography-mass spectrometry (LC-MS).

Reproducibility

Code for the R analysis can be reproduced by following the script in AMBITION_Metabolomics.Rmd. This includes the data normalisation, differential metabolite analysis and all subsequent plots (PCA plot, Correlation plot, Volcano plot).

Metabolic signatures used for pathway analysis where manually assigned based on our a priori knowledge.

Data

The Metabolomics data of the patients myocardial biopsies will be deposited with the manuscript (under revision). LC-MS data aquistion has been performed by the Frezza Laboratory, CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Germany. Input data will be available upon publication in the folder "InputData_AMBITION-Metabolomics":

• AMBITION_RawData.csv (Metabolomics results)
• Template_MetabolicPathways.csv (Metabolite names and associated pathways)

After performing data filtering and normalisation (80%-filtering rule, missing value imputation, total/ion count normalisation) and outlier detection based on quality control (muma analysis, for details see html and folder "Muma"), the results will be saved in the folder "OutputData_AMBITION-Metabolomics"upon publication:

• Sheet2_MVI-TIC-normalised_OutliersMarked.csv

Using the normalised data Sheet2_MVI-TIC-normalised_OutliersMarked.csv, we removed the outliers and

1. calculated the mean of the analytical replicates. The results will be saved in the folder "OutputData_AMBITION-Metabolomics"upon publication:

• Sheet3_MVI-TIC-normalised_Means.csv

2. Performed differential metabolite analysis comparing Ischemia versus Remote using the analytical replicates for the statistics. Here we performed the t-Test and p-value adjustment using Benjamini Hochberg. The results will be saved in the folder "OutputData_AMBITION-Metabolomics"upon publication:

• Sheet4_DMA_ISCHEMIAvREMOTE.csv

Lastly, using the normalised data means Sheet3_MVI-TIC-normalised_Means.csv, we performed differential metabolite analysis comparing impaired LVEF versus preserved LVEF. Here we performed the Mann-Whitney-Wilcoxon Test and p-value adjustment using Benjamini Hochberg. The results will be saved in the folder "OutputData_AMBITION-Metabolomics"upon publication:

• Sheet5_DMA_Impairedvspreserved_LVEF.csv

Figures

Generated figures can be found in the html files or in the folder "Figures_AMBITION-Metabolomics" upon publication.