Metalloprotein metal pools: identification and quantification by coupling native and non-native separations through principal component analysis

A substantial proportion of proteins bind metals but there is no routine method for identifying metalloproteins. High resolution separation techniques generally exploit non-native conditions such that metals can be lost, replaced or acquired during chromatography. The use of reductants and chelators can alter metal-protein speciation, as can oxygen which is also liberated from electrodes. This protocol involves minimal protein fractionation under native conditions, sufficient to identify and quantify the major soluble metalloprotein pools by inductively coupled plasma mass spectrometry. Individual proteins are then further resolved under denaturing conditions. By using principal component analysis (PCA) to compare the change in abundance of each protein with the change in abundance of metal, a candidate metalloprotein is selected and then identified by peptide mass-fingerprinting. The distribution of the metalloprotein across multiple fractions becomes an asset to its subsequent identification. The method is suited to finding and quantifying the major soluble metalloproteins and to studying their metal supply. The protocol can be adapted to extract and separate cytoplasmic proteins under robustly anaerobic conditions