Charge state distributions (CSDs) of proteins in nanoESI mass spectra are affected by the instrumental settings and experimental conditions, in addition to the conformations of the proteins in the analyzed solutions. In the presented study, instrumental and experimental parameters-the desolvation gas flow rate, temperature, pH, buffer (ammonium acetate), and organic modifier (methanol) concentrations-were optimized according to a reduced central composite face experimental design to maximize the separation of CSDs of monoclonal IgG1-antibodies produced by two production systems (CHO and GS-NS0 cell lines). Principal component analysis and Fisher linear discriminant analysis were then used to reduce the dimensions of the acquired dataset and quantify the separation of the protein classes, respectively. The results show that the IgG1-molecules produced by the two production systems can be clearly distinguished using the described approach, which could be readily applied to other proteins and production systems. E lectrospray ionization mass spectrometry (ESI-MS) is a highly suitable technique for structural analysis of various macromolecules, partly because of the possibility of analyzing multiply charged ions from biological molecules, e.g., proteins in solution [1,2]. Further advantages for such analyses are offered by nanoESI-MS [3] (compared with conventional ESI), including reductions in sample consumption, greater tolerance of nonvolatile salts, and the softness of the technique. However, although nanoESI is a preferable ionization method for structural MS analyses of biological macromolecules, nanoESI has been shown to be highly dependent upon the geometry of the nanoflow needle; thus some needle-to-needle irreproducibility is to be expected [4].Charge-state distributions (CSD) of biological macromolecules in ESI-MS are being increasingly employed for exploring their conformations in solutions [4,5]. Changes in protein conformation can result in changes in the CSD in an ESI mass spectrum [6,7]. The mechanism whereby (nearly) desolvated ions are generated from a charged droplet is not completely understood [8]. Proteins acquire more charges in solutions that promote unfolding than the same proteins in solutions that promote folded conformations [7], but it should be noted that other factors than protein compactness may also contribute to differences in CSD patterns [9 -11]. For instance, in addition to altering the conformation of proteins, changes in the solvent also affect the ionization process, i.e., proton-transfer reactions. Thus, the solvent and the operating conditions have different conformational effects on proteins with differing stability during the electrospray process. Hence, understanding the influence of experimental conditions on protein CSDs is important to extract the structural information they may contain.In this study, the effects of selected instrumental and experimental parameters on the CSDs of IgG1-monoclonal antibodies produced by two production systems [Chinese hamster ovary (CHO)...