The reliability of biomarker discovery by means of proteomics has been called into question. It was speculated that "background noise" variation resulting from differences in preparation and handling of samples and proteome dynamics may mask subtle, yet important, differences due to the biological condition. Little is understood about complex proteomes and their variability. A critical aspect of proteomic biomarker research that is largely unexplored is the comparative reproducibility of certain methods such as two-dimensional gel electrophoresis and liquid chromatography/mass spectrometry. In particular, with liquid chromatography/mass spectrometry, it is not known whether variability in peptide quantitation is dependent on any of their several properties such as size, abundance, or hydrophobicity. Such determinations may be critical in properly assessing the value of proteomics data. The fruit fly Drosophila melanogaster was used as a well-controlled multicellular animal model to study the relationship between the background variation and expected changes induced by environmental or genetic factors. The data, gathered by two different proteomics methods, were used to compare and evaluate the reproducibility of the methods. It is reported that there was on average 15 to 18% variability in quantitative measurements of protein abundance using 2-dimensional gel electrophoresis or liquid chromatography/mass spectrometry. Using liquid chromatography/mass spectrometry, peptides with a smaller mass-to-charge ratio were shown to be measured less reproducibly than peptides with a larger ratio. Statistically significant proteomic differences between fly populations could be demonstrated between males and females. In dynamic experiments, less than 0.5% of proteins measured were shown to change after 24 hour starvation of the flies. However, no significant difference in peptide composition could be found for flies fed on a second diet consisting of the standard diet augmented with 10% ethanol. These results suggest that proteomic variability while evident allowed for biomarker discovery using either method for this model system.



College and Department

Physical and Mathematical Sciences; Chemistry and Biochemistry



Date Submitted


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proteomics, methods, drosophila melanogaster, reproducibility