Chapter 8: Techniques for converting metabolomic data for analysis
by Jacopo Troisi, Sean M. Richards, Giovanni Troisi, Giovanni Scala
Before conducting any type of metabolomics data analysis, conversions of the raw data are necessary. This chapter describes the most common techniques used to convert data (aka, pre-treatment operations) obtained from metabolomics investigations. Biological data typically show one or more variables with peculiar statistical characteristics in terms of data distribution (e.g., non-normality or asymmetric distribution). Therefore, it is necessary to transform the data in order to eliminate or mitigate these peculiarities (i.e., normalize the data) that could affect data analysis and interpretation. Furthermore, the multivariate characteristic of information that is common with large datasets from metabolomic investigations, requires data to be comparable and not have a predominant weight in terms of quantitative presence and variability. Data derived from both mass spectrometry and nuclear magnetic resonance are particularly needing of conversion which tend to minimize the effects generated by analytical variability. For these reasons, techniques such as centering and scaling operations as well as transformation are essential steps to correctly prepare the datasets.
Jacopo Troisi is visiting professor of Metabolomics in both Salerno University and University of Sannio in Italy. He is a Research Scientist and COO at the European Biomedical Research Institute of Salerno (EBRIS), co-founded by the Harvard University and the Salerno Medical School. He is also co-founder and CEO at Theoreo srl, a spin-off company of the University of Salerno. Prof. Troisi research is related to metabolomics. In particular, he studies the metabolomic fingerprint of several human diseases to develop diagnostic tools. He has received several international patents for diagnostic tests based on metabolomic profiling. Dr. Troisi has published widely in such peer reviewed journals as Science, Nature Microbiology, Nature Communications, Frontiers in Immunology, Nutrients, BMC Microbiology, Metabolomics, and Scientific Reports.
Sean M. Richards
Department of Biological and Environmental Sciences, University of Tennessee-Chattanooga, Chattanooga, TN 37403 - Department of Biological and Environmental Sciences, University of Tennessee-Chattanooga, Chattanooga, TN 37403, USA; Department of Obstetrics and Gynecology University of Tennessee Health Science Center College of Medicine Chattanooga, TN 37403
Over the last 25 years Dr. Richards has conducted research on the exposure and effects of multiple toxicants on organisms ranging from bacteria to humans. These toxicants include herbicides, insecticides, pharmaceuticals, Bisphenol A, Poly Aromatic Hydrocarbons, Per- and Polyfluoroalkyl Substances, metals, and Poly Chlorinated Biphenyls. Dr. Richards also has experience with the laws and regulations which govern exposure to toxicants through air, soil, and water.
Most recently, Dr. Richards has focused on metabolomics. Specifically, the alterations of metabolomes in response to toxicants or in populations of humans affected by endometrial cancer, congenital malformations, endometriosis, polycystic ovarian syndrome, and fetal central nervous system anomalies. The goal of this research is to determine specific biochemical pathways associated with the affected populations. Ultimately, understanding the changes in the metabolome as a result of disease or intoxication can lead to early detection and personalized treatments.
Giovanni Troisi is an informatic engineer, technical manager of research and development sector for impedentiometry applied to the human body in a big USA company. He supports one of the major Italian government bodies in the Salerno area for the processing of personal, financial and health data of citizens. Finally, he is fully involved in the field of artificial intelligence for the early recognition of new diseases.
Combining his studies in computer engineering with a passion for metabolomics and cellular nutrition, he has developed the technology that has collected and analyzed a huge amount of data coming from University, Hospital and Specialistic diagnostic center tests.
When he isn’t glued to a computer screen, he loves to play sports, enjoy long nature walks with his baby in pouch and trying very hard not to be the worst Russian language pupil in his living area.
He is currently committed to making wellness and health technology personal and within everyone's reach.
Chemist, CTO and cofounder of Theoreo. He deals with the commercial and marketing area. His experience is in the field of advanced analytical technologies, in particular mass spectrometry and chromatographic separation. He coordinates several R&D projects granted by the European Union and managed by Campania Region. These projects deal with mass spectrometry and chromatography applied to various fields: metabolomics, diagnostics, food farming, pollution. From 2006 to 2010 he collaborated with the GCSAR (General Commission for Scientific Agriculture Research, Ministy of Agriculture) in Damasco, in a project dealing with oil and olive production. His current research is related to metabolomics. In particular, he studies the metabolomic fingerprint of several human diseases to develop diagnostic tools. He has received several international patents for diagnostic tests based on metabolomic profiling.