The autocorrelation matrix probing biochemical relationships after metabolic fingerprinting with CE

Abstract

Fingerprinting together with statistical analysis is often employed to compare samples in metabonomic studies of a disease. Correlation algorithms can aid by extracting information based on the variation patterns of key metabolites. This information can be linked to metabolite identification or to specific up/down-regulated biochemical pathways. Matlab-based software employing the Pearson's correlation algorithm was applied to urine electropherograms from 20 mice infected with the schistosoma parasite. The fingerprints were the sum of electropherograms analysed with normal and reverse polarity, in two different modes MEKC and CZE and with two different capillaries (uncoated and polyacrylamide coated) to provide a broad picture of the samples. Hippurate, a metabolite that was depleted in the infected group and is present in both polarities, was chosen as a test variable; it correlated with itself to a p value of <0.000. Phenylacetylglycine, a metabolite shown as over expressed in the disease, was positively correlated to three metabolites in its same pathway with a correlation coefficient of 0.7 and p<0.000 to phenylalanine, 0.7 and p<0.000 to 2-hydroxyphenylacetic and 0.55 and p<0.003 to phenylacetate. The study shows that the autocorrelation matrix is able to provide extra information from data files acquired by CE analyses. It underlined an up-regulated metabolic path by association in the schistosoma infection model.

Improving Metabolite Knowledge in Stable Atherosclerosis Patients by Association and Correlation of GC-MS and1H NMR Fingerprints

“…Finally, a Pearson correlation coefficient, which is obtained by dividing the covariance of the two variables by the product of their standard deviations, was applied with a program developed in house under Matlab. 21 After selecting the variable, the application makes a complete study of correlations among the selected variable and all the others and calculates the statistical significance of the correlations. Results are shown as vectors: (i) correlation vectors among the selected variable and all the others; (ii) vector of p-values of each correlation coefficient previously calculated.…”

Advances in the Biology of Seed and Vegetative Storage Proteins Based on Two-Dimensional Electrophoresis Coupled to Mass Spectrometry

“…2-DE can be routinely applied for the separation of highly complex mixtures of proteins from cell, tissue, organ and organism protein extracts in accordance with their isoelectric point ( pI ) and molecular mass ( M r ) in two successive steps: isoelectric focusing (IEF) in the first dimension and sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) to resolve denatured proteins in the second. The introduction of immobilized pH gradients (IPGs) using bifunctional immobiline reagents enabled us to obtain highly stable pH gradients in the first dimension increasing resolution, reproducibility, the detection of lower abundance proteins and the separation of highly acidic and alkaline proteins [ 97 , 98 ]. Many other technical achievements contributed to the optimization of 2-DE, such as more efficient protein extraction methods, the running of multiple gels in parallel, highly sensitive protein stain methods based on fluorescent dyes compatible with subsequent protein identification by MS technologies, and advanced computer software for the analysis of gel images [ 99 , 100 , 101 , 102 , 103 ].…”

Capillary electrophoresis as a metabolomics tool for non-targeted fingerprinting of biological samples

“…Working with this model, chemometric tools have been applied to improve information extraction, which is probably the weak point of the technique: Matlab-based software employing the Pearson's correlation algorithm was applied to urine electropherograms from 20 mice infected with the schistosoma parasite [28]. The fingerprints were the sum of electropherograms analysed with normal and reverse polarity, in two different modes MEKC and CZE and with two different capillaries (uncoated and polyacrylamide coated) to provide a broad picture of the samples.…”