The core facility metabolomics has a close collaboration with the Bioinformatics Laboratory headed by Prof. dr. Antoine van Kampen located at the Amsterdam UMC; location AMC. This collaboration helps us developing professional tools for the analysis of our complex metabolomics/fluxomics and lipidomics data. Our bioinformaticians developed in-house annotation software tools in the programming languages R and MATLAB for the proper annotation of complex lipid species (figure 1).
![](/upload/f795a09f-c656-477b-8fdd-047dfa3e9923_matlab%20pipeline.png)
Figure 1. The inhouse built MATLAB pipeline for the annotation of lipid species.
In addition to our annotation pipeline we also developed tools for in-depth statistical analysis, visualization tools for the data, pathway analysis and automatic reporting for understanding of the data (figure 2). Using R packages including IsoCorrectoR and multiple in-house made R packages we perform metabolic flux analysis and this produces reliable data and visualizations that allow understanding and interpretation of the metabolome.
![](/upload/f5f0275e-5a9d-45c3-83e9-ecd11012cb97_PipelineOutput.png)
Figure 2. Output of the metabolomics/lipidomics statistical analysis and reporting.
We summarize the results in a short report containing most important findings but also provide you with a quality control report in which we give information about the quality of the data. For most data sets we do a parallel analysis of pool/batch controls that allow us to calculate the variation per metabolite (CV%) which helps with the interpretation of your data.