ES-MS-Analysis of a Pyrrol-Library

The interpretation of mass spectra of compound libraries obtained from direct injection measurements is problematic for two main reasons (i) The yield of ionization of the various components of a library can vary significantly depending upon the structure of the side chain and poorly ionized members are therefore easily overlooked and (ii) even with soft ionization techniques, fragmentation is possible and the additional unexpected peaks impede the interpretation of the mass spectrum. 

This is exemplified on the directly measured library PYL-1 (Fig. 17.10), where the signals of the compounds Py-6 and Py-16 are absent, presumably due to poor ionization yields. Also, compounds Py-13 and Py-17 have the same nominal molecular mass and therefore cannot be differentiated by MS. The fragmentations [M + H-17]+ and [M + H-43]+ of the library molecules lead to a multiplicity of signals complicating the transparency of the mass spectrum. As an example, the signal at m/z 249 can be assigned either to compound 

For these reasons it is not advisable to analyze small-compound libraries by direct injection of the library. On the other hand, the mass spectra of libraries containing several hundreds to thousands of compounds tend to show the expected gaussian-like mass distribution around the average molecular mass. This kind of fingerprinting , which was advanced especially for the analysis of large-peptide libraries, may be accepted for synthesis control of a library, but the evaluation of mass spectra yields only qualitative information. Exact assignment of the compounds is impossible. 

To attain maximum resolution of the components of a mixture by HPLC, the gradient of eluent must be effectively optimized. This procedure can be tedious and time consuming. The rate of sample generation in combinatorial chemistry makes it impossible to find time to optimize the chromatographic conditions for each sample. Fortunately, detection by mass spectrometry alleviates somewhat the need for all compounds to be resolved, since unresolved samples can usually be differentiated on the basis of their molecular 

Compounds with isobaric nominal masses can pose a problem in the analysis of libraries. For example, compounds Py-13 and Py-17 of library PYL-1 (see Section 17.7, Appendix) have the same nominal molecular mass. Using a low-resolution quadrupole mass spectrometer, there is no chance of differentiating between these compounds in the 

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