Although these items represent the analytical ideal, in almost all of these instances the current procedures for chemically analyzing food components and assessing the impact of food components on health fall well short of ideal. This chapter discusses various approaches to food analysis involving advanced and emerging analytical methods and their application. The discussions in this chapter are meant to apply to plants, animals, and microbes. Plants are the most frequently cited example because the introduction of transgenic plants into the food supply is much more pervasive and advanced than either animals or microbes. It should be recognized that improvements are occurring rapidly for both targeted and untargeted (i.e., profiling) methods.
Two basic analytical approaches exist, and each has merit in certain applications. Targeted quantitative analysis is the traditional approach in which a method is established to quantify a predefined compound or class of compounds (e.g., amino acids, lipids, vitamins, or RNAs for specific genes). In contrast, profiling methods involve the untargeted analysis of a complex mixture of compounds extracted from a biological sample with the objective of determining the pattern of detected constituents. For proteins and metabolites this is most often accomplished either by chromatographic (e.g., gas chromatography-mass spectrometry [GC-MS] or liquid chromatography-mass spectrometry [LC-MS]), electrophoretic, or spectral (e.g., nuclear magnetic resonance [NMR]) means, while for nucleic acids methods based on sequence-specific hybridization are used.
The ultimate goal in profiling methods is to quantify and identify all compounds present in a sample (i.e., RNA, protein, and metabolites). This goal is closer to being realized for RNA (the expression of genes) due to advances in gene chip technology and the fact that all DNA and RNA are composed of nucleic acids. Complete quantification and identification of all proteins and metabolites in a sample is still only a theoretical possibility for the reasons discussed in the following sections.
Profiling methods in general are intended to determine the relationship between the pattern of components and a quantitative attribute (e.g., as used widely in the sensory analysis field to evaluate compounds associated with desirable flavor or odor attributes) and to identify differences in the composition of samples by comparing chromatographic and/or spectral patterns derived from complex mixtures. A positive characteristic of the profiling methods is the fact that they allow comparison of patterns of constituents and detection of compositional differences without the requirement for identification of all of the compounds or an understanding of the functions of all genes in an organism.
The inherent difficulties, however, in identifying all of the constituents detected in profiling methods or understanding the activity and potential biological