GENERAL INTRODUCTION 13 1 centrifugation time and force, and temperature of sample storage. For metabolomics and lipidomics, centrifugation (between 2300 and 4000 g for 5–10 min) of whole blood is recommended and for CSF 2000 g at 4°C to separate erythrocytes, leucocytes and platelets.75 For serum samples, the coagulation process should be standardized (brand of tubes, kind of coagulation enhancer, clotting time and ambient temperature).75, 80 On the other hand with stable molecules changes in sample handling do not have to be of large consequences, as has been shown when comparing different aspects (temperature, centrifugation and anti-enzymatic additives) of sample handling in amines in CSF.81 When samples are kept for long-term storage, a storage temperature of -80°C or lower is advised.75, 82 Regarding the patient, aspects of the diet, nutritional state as well as circadian rhythm can all affect the metabolome.75, 83-86 Hence, one should try to keep these factors consistent during sample collection. It is also highly advised to keep track of a person’s medications, smoking habits, daily intake of tea/coffee, and alcohol consumption.75 Despite that these factors are crucial in the data quality of metabolomics research they are often not described in research papers. Figure 1 Coupling of the different -omics, i.e. the genome, epigenome, transcriptome, proteome and metabolome Genomic data can differ at different levels due to, for example, copy number variation (CNV), single nucleotide polymorphisms (SNPs) and mutations, at the genome level; at the epigenome level DNA methylation, histone modification and chromatin accessibility; gene expression and splicing at the transcriptome level; protein expression and post-translational modification at the proteome level; at the metabolome level the metabolic profile. Each variation in each level can be assessed with different techniques either by a targeted approach or an untargeted approach. Adapted from Ritchie et al.79
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