In this paper is reported the synthesis and detailed mass spectrometric and spectroscopic characterization of highly luminescent Au and Ag clusters protected with mixed proteins. Taking advantage of the aggregation tendency of the protein, lysozyme (Lyz), an inter-protein conjugate was made from a physical mixture of two proteins, bovine serum albumin (BSA) and Lyz. Based on matrix-assisted laser desorption/ionization mass spectrometry data, the new cluster is assigned as ∼Au36@BSA-Lyz. This specific system showed a very high red luminescence and the calculated quantum yield was 42% which is the highest to date for such cluster systems. A similar study on an Ag system showed the formation of ∼Ag35@BSA-Lyz when a similar metal and protein concentration was used. By varying the concentration of the Ag precursor, different compositions of the cluster protected by the mixed protein were achieved. Such a system with a high quantum yield can be used for various applications such as sensors for ultralow levels of analytes, fluorescent tags and for tracking biomolecules in real systems. © The Royal Society of Chemistry 2015.