System-level understanding of living organisms has been a long-standing goal of biological sciences. However, it was only recently that this possibility became concrete, by virtue of the development of technology platforms for the production of "omics" data from multiple experimental sources. Data sets such as those from genomics and proteomics are endowing researchers with an unprecedented view of the molecular constituents of cells and of their interactions, forming the basis to pursue the comprehension of how the concerted action of such components can determine biological functions. Within this challenge, bioinorganic chemistry is invested with a renewed significance, being called to place its distinctive subject matter, namely, the study of the interactions between inorganic and biological molecules, in a system-wide perspective. The first step to take in this direction is the construction of "omics" data sets for metalloproteins (metalloproteomics) that can be fruitfully integrated with other protein-centered "omics" data. While looking forward to the progress of high-throughput experimental techniques to accomplish this task, theoretical methods are yielding valuable predictions as to the number of metalloproteins encoded in various genomes. The integrated use of these and others "omics" data can be extremely useful to model complex cellular processes involving metals. Here, we review the current knowledge on copper homeostasis and the assembly of cytochrome c oxidase to exemplify the kind of important processes which need to be studied at the system level. The long-term goal of this approach is the overall description of how metals are framed as essential factors within living cells, which in fact is the ultimate purpose of bioinorganic chemistry.