Increasing conclusiveness of metabonomic studies by chem-informatic preprocessing of capillary electrophoretic data on urinary nucleoside profiles.
Nowadays, bioinformatics offers advanced tools and procedures of data mining aimed at finding consistent patterns or systematic relationships between variables. Numerous metabolites concentrations can readily be determined in a given biological system by high-throughput analytical methods. However, such row analytical data comprise noninformative components due to many disturbances normally occurring in analysis of biological samples. To eliminate those unwanted original analytical data components advanced chemometric data preprocessing methods might be of help. Here, such methods are applied to electrophoretic nucleoside profiles in urine samples of cancer patients and healthy volunteers. The electrophoretic nucleoside profiles were obtained under following conditions: 100 mM borate, 72.5 mM phosphate, 160 mM SDS, pH 6.7; 25 kV voltage, 30 degrees C temperature; untreated fused silica capillary 70 cm effective length, 50 microm I.D. Different most advanced preprocessing tools were applied for baseline correction, denoising and alignment of electrophoretic data. That approach was compared to standard procedure of electrophoretic peak integration. The best results of preprocessing were obtained after application of the so-called correlation optimized warping (COW) to align the data. The principal component analysis (PCA) of preprocessed data provides a clearly better consistency of the nucleoside electrophoretic profiles with health status of subjects than PCA of peak areas of original data (without preprocessing).
Szymańska
E
E
Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera 107, 80-416 Gdańsk, Poland.
Markuszewski
M J
MJ
Capron
X
X
van Nederkassel
A-M
AM
Heyden
Y Vander
YV
Markuszewski
M
M
Krajka
K
K
Kaliszan
R
R
D000465:Algorithms; D014408:Biomarkers, Tumor / Q000652:urine*; D003627:Data Interpretation, Statistical; D019075:Electrophoresis, Capillary / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000378:metabolism / Q000652:urine*; D009705:Nucleosides / Q000652:urine*; D010865:Pilot Projects; D025341:Principal Component Analysis; D012016:Reference Values; D015203:Reproducibility of Results; D049490:Systems Biology / Q000379:methods
D014408:Biomarkers, Tumor; D009705:Nucleosides