At least one third of all proteins are thought to require a metal ion co-factor for their function. Recognition of the importance of metals in biological systems and major advances in analytical instrumentation and technology have led to the emergence of the new research area of metalloproteomics in recent years. Despite this progress, the experimental determination of in-vivo metal cofactors has remained challenging, because this requires elucidation of protein interactions with non-covalently bound metal ions. This critical review highlights current methodological approaches, focusing, in particular, on issues relating to the fractionation and separation of the metalloproteome, including recent experience with metalloproteomics for marine cyanobacteria in our laboratory. Metalloproteomics promises to deliver novel insights into fundamental biological processes in the future, but it is clear that further methodological advances are necessary to exploit the full potential of this emerging research area.