Electrospray ionization coupled with mass spectrometry (ESI-MS) is an important analytical technique for the analysis of polysaccharide derivatives. It can be used to analyze substitution patterns in mixtures of oligomers to recognize heterogeneities, bimodality or blocky sequences. Quantitative analysis is hampered, however, by the fact that compounds of different chemistry and molar mass usually show different ionization efficiencies. In order to study the parameters of influence and to understand whether relative ion intensities in MS follow certain patterns. We analyzed fully O-methylated and fully O-perdeuteriomethylated oligosaccharides as two extreme cases of possible mixed O-Me-/O-Me-d3 by ESI-MS under defined conditions. Binary and complex mixtures of maltooligosaccharide ethers from DP 1 to 7 by were prepared from partially hydrolyzed per-O-methyl-β-cyclodextrin (Me-β-CD) and per-O-deuteromethyl-β-cyclodextrin (Me-d3-β-CD). Reference data for their real compositions were obtained after reductive amination by HPLC–UV. Within the applicable concentration range and with properly adjusted instrumental parameters, relative sensitivities (Me-d3/Me) in ESI-MS remained constant for a respective DP. With increasing DP, the relative sensitivity coefficients decreased from 1.01 for DP 2 to 0.78 for DP 6 for the binary mixtures and showed similar behavior for complex mixtures. The decrease in relative sensitivity coefficients for corresponding Me-d3 and Me derivatives has been overcome by m-amino-benzoic acid labeling and ESI-MS in negative mode or by measuring the original mixtures in nano-ESI-MS. Thus, discrimination probably caused by differences in surface activity and electrophoretic mobility can be leveled by an appropriate tag or formation of smaller droplets as in nano-ESI.