Solution phase isoelectric fractionation in the multi-compartment electrolyser: A divide and conquer strategy for the analysis of complex proteomes
Sample complexity frequently interferes with the analysis of low-abundance proteins by two-dimensional gel electrophoresis (2DGE). Ideally, high abundance proteins should be removed, allowing low-abundance proteins to be applied at much higher concentrations than is possible with the unfractionated sample. One approach is to partition the sample in a manner that segregates the bulk of extraneous proteins from the protein(s) of interest. Solution phase isoelectric focusing in the multi-compartment electrolyser generates fractions of discrete isoelectric point (pI) intervals allowing isolated narrow segments of a proteome to be analysed individually by 2DGE. It is particularly useful for the isolation of low-abundance proteins of extremely basic or acidic pI.
This paper present a comparison of three main algorithms generating initial codebooks with reference to the convergence accuracy and speed. With both the elements considered, splitting methods are found to be more advantageous. Through a study of the common splitting method, an improved one-the orthogonal increment splitting algorithm is proposed. The new method can better utilize the symmetrical property of the speech or image sources, and endow the codewords of the initial codebook with a better distribution in the source space compared with the previous splitting method. The experimental results have confirmed the advantages of the new method, which can effectively eliminate the empty cells and non-typical codewords that may appear in the iteration process, thus achieving a better performance in both convergence speed and accuracy.