Results from SMO Method

1 Estimation of the Separation Parameters The extension of the SDO procedure to 2D separations implies that the 2D map is divided into many strips considered as ID separations on which computations are performed. Different 

On the basis of spot position and intensity, by assuming different critical interdistance Ax o values, experimental points can be obtained and fitted by a straight line (Eq. 4.13) whose slope represents a statistical estimation of m, the estimated number of single components. The values estimated for each ID strip were added to obtain the total number of proteins (Pietrogrande et al., 2002). 

As an example, the data computed on colorectal adenocarcinoma cell line map (DLD1 HUMAN) (Demalte-Annessi et al., 1999 Pietrogrande et al., 2002). (Fig. 4.1a) are reported as follows. 

Even if the number of proteins present in the map is low, the method provides a helpful tool to estimate m values with good accuracy—expressed as the relative error of the estimated m vs. real m values, s%—and precision—as relative standard deviation CV% on 50 runs—in particular, if the division procedure into variable number of strips is used (Pietrogrande et al., 2002). 

FIGURE 4.12 Experimental 2D-PAGE map of a neuroblastoma xenograft implanted in mice. The circles indicate the spots identified by MS analysis. Reproduced from Campostrini et al. (2005) with permission from Wiley-VCH Verlag GmbH. 

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