Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" - specifically, the study of their small-molecule metabolite profiles The metabolome represents the collection of all metabolites in a biological organism, which are the end products of its gene expression. Thus, while mRNA gene expression data and proteomic analyses do not tell the whole story of what might be happening in a cell, metabolic profiling can give an instantaneous 'snapshot' of the physiology of that cell. One of the challenges of systems biology is to integrate proteomics, transcriptomics, and metabolomics information to give a more complete picture of living organisms.
The word metabonomics is also used, particularly in the context of drug toxicity assessment. There is some disagreement over the exact differences between 'metabolomics' and 'metabonomics'; in general, the term 'metabolomics' is more commonly used. 
Metabolic biochemists have arguably been 'doing metabolomics' for decades. It has been suggested that the concept of metabolomics is foreshadowed by Linus Pauling's work toward "orthomolecular medicine" and his hypotheses regarding the predictive capacity of chromatographic profiling of bodily fluids for detection and diagnosis of human disease. However, the common use of the term and the identification of metabolomics as a distinct scientific field is much more recent, with the earliest published references in the scientific literature dating from the late 1990s and early 2000s.
It should be noted that many of the bioanalytical methods used for metabolomics have been adapted (or in some cases simply adopted) from existing biochemical techniques, and thus there are not always clear distinctions between studies that are described as metabolomic and studies that are concerned with metabolism. However, metabolomic research has two characteristics:
1. Metabolites are profiled without bias towards a specific metabolite or group of metabolites
2. Relationships between the metabolites are characterized, currently mostly by multivariate methods.