Biomolecular method comparison

The ion source used for the generation of biomolecular parent ions is critical, and only recently have the so-called soft ionization methods been developed.2 Electron-impact ionization sources fall into the category of hard sources, whereby the sample must be in the vapor phase initially, and the ionization process produces a very large number of fragments. Soft methods were introduced to overcome the problems associated with the thermal instability and involatility of macromolecular analytes. Soft ionization produces few fragments under relatively mild conditions. In Table 15.1 a comparison is shown between the three main soft ionization methods some of these values are strongly dependent on individual mass spectrometer configurations and the desired resolution. 

Although the interface of a TOF spectrometer with ESI has been traditionally difficult, orthogonal injection has recently proven to be a good method to enable the ESI method to be coupled with a TOF spectrometer [475]. This also gives possibilities of studying biomolecular complexes. ESI has also recently been coupled to ion mobility spectrometry, which enables a higher resolution in comparison with... 

Ewald summation presented above calls for the calculation of AP terms for each of the periodic boxes, a computationally demanding requirement for large biomolecular systems. Recently, Darden et al. proposed an N log N method, called particle mesh Ewald (PME), which incorporates a spherical cutoff R. This method uses lookup tables to calculate the direa space sum and its derivatives. The reciprocal sum is implemented by means of multidimensional piecewise interpolation methods, which permit the calculation of this sum and its first derivative at predefined grids with fast Fourier transform methods. The overhead for this calculation in comparison to Coulomb interactions ranges from 16 to 84% of computer time, depending on the reciprocal sum grid size and the order of polynomial used in calculating this sum. 

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