Mass deconvolution

The full-scan mode is needed to achieve completely the full potential of fast GC/MS. Software programs, such as the automated mass deconvolution and identification system (AMDIS), have been developed to utilize the orthogonal nature of GC and MS separations to provide automatically chromatographic peaks with background-subtracted mass spectra despite an incomplete separation of a complex mixture. Such programs in combination with fast MS data acquisition rates have led to very fast GC/MS analyses. 

A large amount of fuel and environmentally based analysis is focused on the determination of aliphatic and aromatic content. These types of species are often notoriously difficult to deconvolute by mass spectrometric means, and resolution at the isomeric level is almost only possible by using chromatographic methods. Similarly, the areas of organohalogen and flavours/fragrance analysis are dominated by a need to often quantify chiral compounds, which in the same way as aliphatic... 

An advantage of the microbore gas chromatrography/time-of-flight mass spectrometry (GC/TOFMS) method over the other two approaches is that separation efficiency need not be compromised for speed of analysis. The rapid deconvolution of spectra ( scan rate ) with TOFMS makes it the only MS approach to achieve several data points across a narrow peak in full-scan operation. However, the injection of complex extracts deteriorates performance of microbore columns quickly, and an increased LOD and decreased ruggedness result. Microbore columns may be used in water analysis if the LOD is sufficiently low, but they can rarely be used in real-life applications to complicated extracts. 

If we consider only a few of the general requirements for the ideal polymer/additive analysis techniques (e.g. no matrix interferences, quantitative), then it is obvious that the choice is much restricted. Elements of the ideal method might include LD and MS, with reference to CRMs. Laser desorption and REMPI-MS are moving closest to direct selective sampling tandem mass spectrometry is supreme in identification. Direct-probe MS may yield accurate masses and concentrations of the components contained in the polymeric material. Selective sample preparation, efficient separation, selective detection, mass spectrometry and chemometric deconvolution techniques are complementary rather than competitive techniques. For elemental analysis, LA-ICP-ToFMS scores high. 

Association Fran aise de Normalisation French Association for Standardisation (Paris, France) Automated Mass Spectral Deconvolution and Identification System (NIST)... 

The behavior of D2 in the Raman experiments is strongly correlated with the Q4 chemical shift, 6, in the NMR spectra. 6 equals about -110 to -111 ppm when D2 is absent or when it exhibits low relative intensities comparable to those in conventional vitreous silica, for example the 50 and 1050°C sample spectra and the rehydrated 600°C sample spectrum. From the regression equation cited above -110 to -111 ppm corresponds to - 147 to 149°, values quite close to the average in conventional v-Si02, 151° (4 ). The average 64 is shifted downfield to about -107 ppm in the 600°C sample in which D2 is observed to be quite intense. Deconvolution of this peak reveals two Q4 resonances at -110 and -105 ppm. -105 ppm corresponds to - 138°, which is very near the equilibrium 4> calculated for the isolated cyclic trisiloxane molecule, HgSi303, ( = 136.7°) (46). The positions of the Q2 and Q3 resonances, however, appear to be totally unaffected by the presence or absence of D2 (as shown in the 600°C CP MASS sample spectrum). 

For these reasons we have developed a different approach that measures differential expression of intact proteins.21 In this approach the proteins are extracted from the cell, separated on an HPLC column, ionized via electrospray, and automatically deconvoluted into their respective uncharged nominal masses. By this methodology it is then possible to obtain accurate, intact protein profiles of the individual strains of bacteria. Because the masses of the detected proteins are accurate to +2 Da from run to run, it is possible to subtract protein profiles from known strains to quickly identify differences in protein expression among newly mutated strains. 

Figure 10.4 All spectra obtained between 20 and 66 minutes are combined into a single spectrum and then deconvoluted using MaxEnt 1. The resulting molecular weight spectrum is noisy and hampers the identification of low abundance proteins. The asterisks indicate where proteins of mass 7274 and 10652 should be observed but are not.

Upon completion of the ProteinTrawler program, the text hie contains a cumulative hst of all the protein masses that were observed upon deconvolution of the individual summed spectra. This text hie records mass, intensity, and retention time. The retention time information is held in the text hie for... 

Figure 10.6 Single representative cellular protein spectrum of E. coli K12 generated by deconvoluting the spectra in 30-second intervals from 20 minutes to 66 minutes. The asterisks indicate where proteins of mass 7274 and 10,652 are observed.

The first application of ANNs to pyrolysis mass spectra from biological samples was by Goodacre, Kell, and Bianchi.96,97 This study permitted the rapid and exquisitely sensitive assessment of the adulteration of extra-virgin olive oils with various seed oils, a task that previously was labor intensive and difficult. Since this study other laboratories have increasingly sought to apply ANNs to the deconvolution and interpretation of pyrolysis mass spectra, the aim being to expand the application of the PyMS technique from microbial characterisation to the rapid and quantitative analysis of the chemical constituents of microbial and other biological samples. 

Goodacre, R. Neal, M. I Kell, D. B. Quantitative analysis of multivariate data using artificial neural networks A tutorial review and applications to the deconvolution of pyrolysis mass spectra. Zbl. Bakt. 1996,284, 516-539. 

Sinha, A.E., Hope, J.L., Prazen, B.J., Fraga, C.G., Nilsson, E.J., Synovec, R.E. (2004a). Multivariate selectivity as a metric for evaluating comprehensive two-dimensional gas chromatography-time-of-fhght mass spectrometry subjected to chemometric peak deconvolution. J. Chromatogr. A 1056, 145-154. 

Because online separations provide such a wealth of information about target proteins, interpretation becomes of critical importance in order to make full use of the data. The first step in any analysis of LC-MS data involves integration and deconvolution of sample spectra to determine protein mass and intensity. In manual analysis (Hamler et al., 2004), users identify protein umbrellas, create a total ion chromatogram (TIC), integrate the protein peak, and deconvolute the resulting spectrum. Deconvolution of ESI spectra employs a maximum entropy deconvolution algorithm often referred to as MaxEnt (Ferrige et al., 1991). MaxEnt calculates... 

Ferrige, A. G., Seddon, M. J., Jarvis, S. (1991). Maximum-entropy deconvolution in electrospray mass-spectrometry. Rapid Commun Mass Sp. 5(8), 374-377. 

The ESI-MS of an intact protein yields a series of ions with mfc values corresponding to sequentially charged species (Fenn et al., 1989). Algorithms and software for the deconvolution of these peaks into a single neutral mass have been available for many... 

FIGURE 13.3 Raw and deconvoluted mass spectra of a yeast ribosomal protein (L16) from a 2DLC(SCX/RP)/MS experiment were obtained, where mass spectral adducts were observed because of insufficient washing of the second-dimension RP column (Panel a, 7 column volumes of wash). Panel b shows mass spectra for the same protein from an experiment with sufficient second-dimension wash volumes (Panel b, 14 column volumes of wash). 

The central engine of this data workflow is the process of spectral deconvolution. During spectral deconvolution, sets of multiply charged ions associated with particular proteins are reduced to a simplified spectrum representing the neutral mass forms of those proteins. Our laboratory makes use of a maximum entropy-based approach to spectral deconvolution (Ferrige et al., 1992a and b) that attempts to identify the most likely distribution of neutral masses that accounts for all data within the m/z mass spectrum. With this approach, quantitative peak intensity information is retained from the source spectrum, and meaningful intensity differences can be obtained by comparison of LC/MS runs acquired and processed under similar conditions. 

FIGURE 13.5 The total ion chromatogram and deconvoluted protein mass map for a ID LC/MS analysis of yeast ribosomal proteins. The bubble size is proportional to component intensity. 

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