Fingerprints from fragments

Static secondary ion mass spectrometry (SIMS) [31] has been applied to structural characterisation [32-35] and surface analysis of polymers [36, 37]. Polymers can be identified from fingerprint spectra or from fragments characteristic of the backbone and pendant groups. Liquid matrix SIMS-FAB-MS has provided only approximate oligomer distribution. 

These signals in the NOE spectra therefore in principle make it possible to determine which fingerprint in the COSY spectrum comes from a residue adjacent to the one previously identified. For example, in the case of the lac-repressor fragment the specific Ser residue that was identified from the COSY spectrum was shown in the NOE spectrum to interact with a His residue, which in turn interacted with a Val residue. Comparison with the known amino acid sequence revealed that the tripeptide Ser-His-Val occurred only once, for residues 28-30. 

Exonuclease An enzyme that cleaves nucleotides from either the 3 or 5 ends of DNA or RNA. Fingerprinting The use of RFLPs or repeat sequence DNA to establish a unique pattern of DNA fragments for an individual. 

Figure 2.4. Peptide fingerprinting by MALDI-TOF mass Spectrometry. Proteins are extracted and separated on by 2D gel electrophoresis. A spot of interest is excised from the gel, digested with trypsin, and ionized by MALDI. The precise mass of proteolytic fragments is determined by time-of- flight mass spectrometry. The identity of the protein is determined by comparing the peptide masses with a list of peptide masses generated by a simulated digestion of all of the open reading frames of the organism.

As illustrated in the next section, the use of biological fingerprints, such as from a BioPrint profile, provides a way to characterize, differentiate and cluster compounds that is more relevant in terms ofthe biological activity of the compounds. The data also show that different in silico descriptors based on the chemical structure can produce quite different results. Thus, the selection of the in silico descriptor to be used, which can range from structural fragments (e.g. MACCS keys), through structural motifs (Daylight keys) to pharmacophore/shape keys (based on both the 2D structure via connectivity and from actual 3D conformations), is very important and some form of validation for the problem at hand should be performed. 

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