Mass spectra simulation

Software is also being developed to simulate mass spectral data of given structure. One such program, MASSIMO (mass spectra simulator), has been developed in parallel with the FRANZ algorithms and gives predictions for both peaks and intensities of fragment ions. 

B. Fan, H. Chen, M. Petitjean, A. Panaye, J.-P. Doucet, H. Xia, and S. Yuan. New strategy of mass spectrum simulation based on reduced and concentrated knowledge databases. Spec-trosc. Lett., 38(2) 145-170, 2005. 

Fig. 7. Simulated (high resolution m/z values calculated, intensity ratios of the highest peaks taken from [89]) upper part of mass spectrum of a TCBT isomer...

Figure 9 (a) ESI-FTICR broad-band mass spectrum of a library thought to be H-Gly-pTyr-Xxx-Xxx-Xxx-Cys-OH where Xxx can be any one of the naturally occurring amino acids with the exception of Cys and Trp. (b) A simulated mass spectrum of H-Gly-pTyr-Xxx-Xxx-Xxx-Cys-OH. (c) A computer-simulated spectrum of library H-Xxx-Xxx-Xxx-Cys-OH where Xxx can be any one of the naturally occurring amino acids with the exception of Cys and Trp. (Reprinted from Ref. 92.)... 

The aim of BPS-MS approach presented here can be summarized by comparing the simulated receiver operator characteristic (ROC) curves shown in Figure 1. Each additional dimension of analysis (a distinct pulse shape, that yields distinct mass spectrum) enlarges the area under the curve and therefore the confidence of the measurement. 

The SG uses the empirical formula along with Goodlist and Badlist to generate exhaustively but without redundancy a list of candidate structures for the form of the substance which gave rise to the mass spectrum. These candidates, consonant with the empirical formula, Goodlist and Badlist are then given as input to the third phase of HDP, the spectral simulator, called the Predictor. 

Mass spectra of the partial methanolyzed PBA/PBT/PBSe terpolyester (a) experimental FAB mass spectrum (b) simulated mass spectrum. (Peak assigments are reported in Table 7.2.) (Reprinted with permission from Ref. 72, Copyright American Chemical Society.)... 

Taking into account that the most abundant ion in one distribution of the native PEG was not necessarily the same in the corresponding distribution of the product and that the ionization mechanism was fluctuating, automatic simulation of PEG product spectra by simply shifting the ion distributions recorded in native PEG mass spectrum was not possible. 

FIGURE 9.14 (a). Simulated mass spectrum of m/z 491 from rhodamine 101 striking the end-cap electrode using model geometry 1. A significant number of ions, ca 20% of the total number and identified as m/z 491, are pre-ejected before the main peak and are observed at ca 2 Th lower than the main peak, (b), A plot of the apparent m/z-value with respect to ion initial axial position (zj) for the individual ions contributing to the simulated mass spectrum in panel (a). 

The Pt clusters made up of 4 to 6 Pt atoms protected by N,N-Dimethylformamide were synthesized by Kawasaki et al. by previously reported process. These clusters were photo - luminescent with their emission maximum dependent upon the excitation wavelength. The composition of these clusters was determined by MALDI MS by ligand exchanging them with 2-mercapto-benzothiazole (MBT). The mass spectrum shown in Fig. 8A, consisted of a peak corresponding to Pt5(MBT)y as the dominant signal and it was in agreement with the simulated mass obtained in isotopic analysis. The clusters with 4 and 6 Pt atoms were also present which were assigned as shown in the Fig. 8A. °... 

As mentioned earlier, fragmentation in a mass spectrometer generally follows known reaction schemes. We will use this knowledge during calculation of a match value for structure candidate M with respect to experimental mass spectrum I. The calculation is similar to that for molecular formula candidates. However, in the case of structural formulas we can considerably restrict the set of possible fragment molecular formulas jSj. We will consider only such molecular formulas for which fragments exist that are derived from M by successive ionization and fragmentation reactions. To simulate these we go back to the previous work in Section 2.3. 

The parent ion of 2-butanone has m/z = 72 and it can fragment on both sides of the carbonyl. One cleavage leads to daughter ions m/z = 43 and m/z = 29. Cleavage on the other side of the carbonyl leads to daughter ions m/z = 15 and m/z = 57. All five of these ions are drawn on the simulated mass spectrum. 

Simulation of part of a mass spectrum of [ReBr(C0)5]. The weak peaks arise from ions containing or 0. 

Of course. Figure 2.7 shows the trajectories for only one particular set of entry conditions. The ion trajectory is actually very dependent on these conditions, and also on the relative phase of the RF drive (fo in equations (2.1.10) and (2.1.11)). By varying the conditions systematically, one can determine the fate of a large number of ions, and thus generate a simulated mass spectrum. 

Of course, it would be near impossible to generate a real mass spectrum to correspond with those in Figure 2.9, because the ion distribution is quite artificial. Figure 2.10 shows a mass spectrum of indium from a modern commercial ICP-MS. The sample was 100 ppb of indium in 2% nitric acid. The main peaks, at 112.9 amu and 114.9 amu, are from the isotopes In and In. Also plotted is the simulated peak for ions of mass 114.9 amu. It is clear that the model accounts for the basic features of the observed mass spectrum. 

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