pioneered the field of MS characterization of ultra-small nanoparticles by using laser desorption ionization (LDI) to study dodecanethiol-protected gold NCs having masses in the range of 27-93 kDa. Ionization techniques softer than LDI, especially matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI), later became more popular to better preserve intact ligandprotected clusters. As they rely on radically different ionization processes, these two techniques allow to address the diversity of the chemical nature of the ligands used to stabilize NCs. ESI is particularly well-suited to ionize water soluble nanoclusters, and has the advantage to cause reduced fragmentation as compared to MALDI, even for fragile particles. However, ESI usually yields multicharged species, resulting in more complex spectra. MALDI ionization is then popular to study nanoclusters with high molecular weights. For instance, it has been used to assign approximate compositions to very large nanoclusters with mass ranging from 300 to 400 kDa. In general MALDI performs better than ESI for organic-soluble nanoclusters, but the choice of the matrix is critical. For instance, Dass et al. proposed trans-2-[3-(4-tert-butylphenyl)-2-methyl-2propenylidene] malononitrile (DCTB) as a matrix for MALDI-MS of intact Au25(PET)18 clusters. Then Kawasaki and coworkers reported a new MALDI matrix, e.g. α, β-diphenylfumaronitrile (DPF) for thiol-protected gold clusters. As biocompatibility is key to several applications of NCs, recent strategies have been proposed to replace small organic thiolated ligands by macromolecular templates, like proteins. Most of these protein-protected NCs have been characterized by MALDI-MS using standard matrices compatible for proteins, such as sinapinic acid (SA), 2,5-dihydroxybenzoic acid (DHB), or α-cyano-αhydroxy cinnamic acid (CHCA). These matrices contain carboxylic groups favouring proton-transfer to the analyte, and thus the formation of protonated species. Even protein signal in negative mode using the same matrices have also been reported. Consequently, most MS investigations of protein-protected clusters were performed in the positive ion mode. Besides, MALDI-MS investigations on BSA protected gold nanoclusters using similar synthesis protocols led to some dispersion in the determination of the gold atoms number. This dispersion may be influenced by sample preparation issues, e.g. use of different matrices and deposition protocols. The aim of the present work is to evaluate the effect of MALDI matrices for the MS characterization of proteinprotected nanoclusters in both negative and positive ion modes. To this end, the MALDI response of a series of NCs of different metals, stabilized by different proteins, have been compared using different matrices.