Graham Wood (Macquarie University and Warwick Systems Biology)

Normalization of ratio data

Quantitative mass spectrometry techniques are commonly used for comparative proteomic analysis in order to provide relative quantitation between samples. For example, in attempting to find the proteins expressed in ovarian cancer, the quantities of a given protein are assessed by mass spectrometry in separate samples of both cancerous and healthy cells. To account for the variable “loading” (the total volumes of samples) from one sample to the other, a normalization procedure is required. A common approach to normalization is to use internal standards, proteins that are assumed to display only minimal changes in abundance between the samples under comparison. A normalization procedure then allows adjustment of the data, so enabling true relative quantities to be reported.

Normalization is determined by centring the symmetrized ratio (say, cancerous over healthy) internal standards data. This presentation makes two contributions to an understanding of ratio normalization. First, the customary centring of logarithmically transformed ratios (frequently used, for example, in microarray analyses) is shown to attend not only to centring but also to minimisation of the spread of the symmetrized data. Second, the normalization problem is set in a larger context, allowing normalization to be achieved based on a symmetrization which carries the ratios to approximate normality, so increasing the power with which under or over-expressed proteins can be detected. Both simulated and real data will be used to illustrate the new method.