Fragments detection

As mentioned above, all data in the analysis are from fragment screens using NMR spectroscopy to detect fragment binding... 

The main challenge for any fragment screening method is the detection of weak binders. The methods commonly used to detect fragments can be broadly broken down into biophysical and functional assays. 

The peak intensities are calculated automatically. The sizes of the detected fragments are automatically determined using an internal standard. 

For example, full-scan mass spectra of buspirone contain an abundant [M+H]+ ion signal with little detectable fragmentation. The product ion spectrum reveals product ions and neutral losses associated with diagnostic substructures of buspirone (Figure 6.25). The product ion at mlz 122, for example, is indicative of the pyrimidine substructure. The presence of this ion in the product ion spectrum of a metabolite indicates a structure that contains the pyrimidine substructure. Similarly, the mlz 180 product ion is diagnostic of the azaspirone decane substructure, and the neutral loss of 164 (producing the mlz 222 product ion) is diagnostic of the butyl azaspirone decane dione substructure. 

A common drawback of these two instruments is the impossibility to observe any metastable fragmentation which occurs in the first mass analyser between the source and the first reflectron. Because these fragment ions penetrate in the first reflectron, they do not arrive at the deflection gate and collision cell at the same time as their precursors. Thus, they do not contribute to the detected fragment ions and are not recorded in the fragmentation spectrum of the selected ion. Since such metastable fragmentations are generally not minor processes, this reduces the efficiency of these mass spectrometers. 

Tandem mass spectrometry (MS-MS) using quadrupole mass analyzers or ion-trap analyzers facilitate the conducting MS-MS experiments and increases the sensitivity of detection. Fragmentation patterns of anthocyanins generally show the loss of a glycoside or... 

The AFLP has the power of PCR and the solidity of RFLP analysis. As the AFLP is highly reproducible and has a deep enough resolution due to the number of estimable detected fragments this technique allows us to analyze the strains at the intraspecies level. With this technique we can carry out epidemiological studies or can generate a database for routine identification. We proved that its application is very usefiil in the determination of the route of an infection or in the correct identification of pathogenic yeasts. 

Full-scan mass spectra generally contain an abundant [M - - H] ion signal with little detectable fragmentation. Product-ion spectra are obtained to reveal product ions and neutral losses that are associated with diagnostic substructures of the buspirone molecule. 

Boyd, R. K., Porter, C. J. and Beynon, J. H. Linked-scan laws to detect fragmentations in the second field-free region of a double-focussing mass spectrometer. Int.. Mass Spectrom. Ion Phys. 44 199-214, 1982. 

For example, given an initial fragment, labeled at the 5 -end, that has the sequence 32P-GCTGCTAGGTGCCGAGC, partial cleavage at (and removal of) the G residues will yield the following detectable fragments ... 

In 1975 Edward Southern developed a technique that is widely used to detect fragments of DNA. This technique, known as Southern blotting,first requires an electrophoretic separation of DNA or DNA fragments by AGE. Next a strip of nitrocellulose or a nylon membrane is laid over the agarose gel, and the DNAs or DNA fragments are... 

In analogy with the techniques of coupling GC and LC to a mass spectrometer for the identification of the components of a mixture, McLafferty and co-workers [106a,173] designated as MS/MS the method of detecting fragmentations outside the source, as discussed previously. 

Typically, the LC-MS full scan mass spectra of a drug molecule contain abundant [M + H]+ ions with little detectable fragmentation. The product ion mass spectrum contains product ions associated with diagnostic substructures of the drug molecule. There is no need, and more importantly, there is no time in a drug discovery setting to identify all fragment ions observed in the product ion mass spectra. Instead, streamlined approaches based on standard methods and structural template motifs are used [89],... 

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