Fragment libraries comparison

Comparison of Hits, Nonhits, and the Entire Fragment Library... 

Table 3.2 Comparison of selected fragment libraries reported in the literature and on company WEB sites. 

Nepeta (Lamiaceae) is a genus of perennial or annual herbs found in Asia, Europe and North Africa. About 250 species of Nepeta are reported of which, 67 species are present in Iran. Some species of this genus are important medicinal plants and their extracts have been used for medicinal purposes. Aerial parts of Nepeta sintenisii Bornm. was subjected to hydrodistillation and the chemical composition of isolated essential oil has been analyzed by GC/MS method for first time. Identification of components of the volatile oil was based on retention indices relative to n-alkanes and computer matching with the Wiley275.L library, as well as by comparison of the fragmentation patterns of the mass spectra with those reported in the literature. 

Only the particle-beam interface produces El spectra for direct comparisons with computerized library spectra of fragmentation patterns. The other systems enable the relative molecular mass (RMM) of analytes up to 105 and above to be established. An example of an HPLC-APCI separation and identification of some benzodiazepine tranquillizers is shown in Figure 4.39. The most appropriate choice of LC-MS interface for a particular... 

Electronic databases of the mass spectral fragmentation patterns of known molecules can be rapidly searched by computer. The pattern and intensity of fragments in the mass spectrum is characteristic of an individual compound so comparison of the experimental mass spectrum of a compound with those in a library can be used to positively identify it, if its spectrum has been recorded previously. 

Thus, the presence of the methoxyphenols in pyrolysis products indicates that lignin-like components have survived for approximately 3(X) million years. That the specific peak was indeed methoxyphenol was determined by retention time and by examination of the fragment ions at m/z 109 and 81. Similarly, the verification of the presence of methy thoxyphenol was made by retention time and by examination of fragment ions at nVz 123 and 95. Dir t comparison of mass spectra to library spectra of audientic methoxyphenols was not possible due to the trace quantities and the complexity of die pyrolysis mixture in the retention-time windows for elution of the methoxyphenols. 

Tor reference. Positive identification can be made only by collecting the compound or transierring it as it elutes directly into another apparatus for analysis by other means, such as infrared or ultraviolet spectroscopy, mass spectrometry, or nuclear magnetic resonance. Commercially available apparatus is available which combines in a single unit both a gas chromatograph and an infrared, ultraviolet, or mass spectrometer for routine separation and identilicalion. The ancillary system may also be microprocessor-based, with an extensive memory for storing libraries of known infrared spectra or fragmentation patterns (in the case of mass spectrometers). Such systems allow microprocessor-controlled comparison and identilicalion of detected compounds. 

A common method for identification of organic compounds is mass spectrometry (MS) in combination with GC. After separation of the component by GC the mass spectrometer transform the analyte into gaseous ions in vacuum in the ion source. For electron impact ionization this results in different mass fragmentation patterns with different mass-to-charge ratios (m/z). From this fragmentation pattern it will be possible to identify the compound by comparison with commercial mass spectral libraries. Identification of unknown compounds can be facilitated by... 

Generally, the mass spectra corresponding to peaks in the gas chromatograms obtained in the El mode at 70 eV are assigned by comparisons with mass spectral libraries. The fragments were assumed to be characteristic of the original structure (Galletti and Bocchini, 1995 Schulten, 1996). However, one often-described disad-... 

The GC is often connected to a mass spectrometer. Mass spectrometry (MS) breaks samples apart and separates the ionized fragments by mass and charge. Vast libraries of comparison fragments make computer-aided identification of materials possible even when the sample is very small. Most forensic laboratories have access to a combined gas chromatograph/mass spectrometer (GC/MS). High pressure liquid chromatography (HPLC) separates many types of drugs and may also be combined with MS. 

The computer can also calculate the possible compositions of ions of a given mass, taking into account only the elements in the molecular formula. For example, if a compound is known to contain only CHON as elements, a fragment detected at m/z 39 can have only C2HN or C3H3 as its elemental composition. More examples can be found in Appendix 5. The computer can also calculate for a given molecular formula the theoretical relative abundances within the isotopic cluster for comparison with experimental values. It can also compare the spectra that it observes with a library of spectra. 

The current chemical space is occupied by compounds isolated from nature, synthesised by conventional solution phase synthesis, solid phase combinatorial synthesis and by smaller fragment based libraries. These libraries vary significantly both in their size and complexity. The comparison of diversity of these libraries and their impact as drug leads is reviewed in this chapter. 

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