ES-MS-Analysis of Single Compounds

When working on combinatorial synthesis, differences in analyzing combinatorial compounds rather than peptides or oligonucleotides become apparent. These arise from the greater variety of reagents used and different reaction types which require an adaptation of several reaction parameters, e.g., reaction time, temperature, etc. A further reason is the development of a huge number of different resin types and linkers tailored for combinatorial synthesis, but which were not necessary in peptide chemistry. 

A problem which arises after cleavage not only from polystyrene-based polymeric carriers is the presence of impurities derived presumably from linker or resin components [57]. The occurrence of these impurities hampers routine product analysis and may have considerable influence also on the screening assay. In the mass spectrometric analysis, they can compete with poorly ionizable products, thus inhibiting a reliable analysis. At worst, they may even preclude detection of the expected compound, leading to a misinterpretation of the synthesis results. It has been found that the extraneous signals in the mass spectra are primarily dependent upon the type of resin used. Differences between analogous resins from different suppliers, or even different charges are also observed. As yet, it has not been possible to characterize these impurities with the methods of mass spectrometry and NMR. 

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