PCB 5530 Antje Thamm & Tom Niehaus Fall 2015
Metabolomics PCB 5530 Antje Thamm & Tom Niehaus Fall 2015 Learning Outcomes Day 1 (Antje Thamm) Day 2 (Tom Niehaus)
Lecture - Learn the basics of metabolomics - Understand the limitations of metabolomics - Things to consider when using metabolomics for your own research Day 2 (Tom Niehaus) Activity 1: Identifying an unknown peak Activity 2: Analyzing a metabolomics dataset Definitions and Background
Metabolome = the collection of all metabolites in a sample All low molecular weight (< 2000 Da) organic molecules in a sample such as a leaf, fruit, seedling, serum, urine, etc. Sugars Nucleosides Organic acids Ketones Aldehydes Amines Amino acids Small peptides Fatty acids Isoprenoids Phenols Alkaloids Drugs and pesticides Definitions and Background
Metabolomics = high-throughput analysis of metabolites Metabolomics is the simultaneous measurement of the levels of a large number of cellular metabolites (typically several hundred). Many of these are not identified (i.e. are just peaks in a profile). Not hypothesis driven snapshot Definitions and Background Definitions and Background
Scope Accuracy Metabolomics -measure many compounds - relative measurements Metabolic profiling -measure a set of related compounds (e.g. phosphate esters) Targeted analysis -measure a specific compound -absolute quantification is possible Definitions and Background History and Development
Metabolic profiling is not new.Profiling for clinical detection of human disease using urine samples has been carried out for Centuries. This urine wheel was published in 1506 by Ullrich Pinder, in his book Epiphanie Medicorum. The wheel describes the possible colors, smells and tastes of urine, and uses them to diagnose disease. eg maple syrup urine disease: metabolism of branched chain amino acids; ketones are detected in urine; diabetics secrete sugars into urine Nicholson, J. K. & Lindon, J. C. Nature 455, 10541056 (2008). Definitions and Background History and Development
Advanced chromatographic separation techniques were developed in the late 1960s. Linus Pauling published Quantitative Analysis of Urine Vapor and Breath by Gas-Liquid Partition Chromatography in 1971 Chuck Sweeley at MSU helped pioneer metabolic profiling using gas chromatography/ mass spectrometry (GC-MS) Plant metabolic biochemists (e.g. Lothar Willmitzer) were among other early leaders in the field. Metabolomics is expanding to catch up with other multiparallel analytical techniques (transcriptomics, proteomics) but remains less developed and less accessible. Definitions and Background
Plant Metabolome Size It is estimated that all plant species combined contain 90, ,000 compounds. Each individual plant species contains about 5,000 30,000 compounds. e.g. ~ 5,000 in Arabidopsis The plant metabolome is much larger than that of yeast, where there are far fewer metabolites than genes or proteins (