The word metabolome appears to be a blending of the words "metabolite" and "chromosome". It was constructed to imply that metabolites are indirectly encoded by genes or act on genes and gene products.  The term "metabolome" was first used in 1998  and was likely coined to match with existing biological terms referring to the complete set of genes (the genome), the complete set of proteins (the proteome) and the complete set of transcripts (the transcriptome). The first book on metabolomics was published in 2003.  The first journal dedicated to metabolomics (titled simply "Metabolomics") was launched in 2005 and is currently edited by Prof. Roy Goodacre.  Some of the more significant early papers on metabolome analysis are listed in the references below.