Quantitation of leishmania secreted proteins in Cm. Conditioned medium (Cm)/cell associated (CA) ratios from each of four independent analyses were normalized to the ratio for that of histone H2B followed by log normal (Ln) transformation (see Additional data file 2). Mean values across the four experiments for each protein identity were calculated as described in Materials and Methods. GraphPad Prism 4.0 was then used to calculate the mean and standard deviation (SD) of all Cm/CA values for all proteins found in leishmania Cm (mean = 1.39, SD = 0.85). The same program generated a frequency distribution of the mean Cm/CA values based on the relative frequency of each value within the dataset. Proteins with mean Cm/CA values greater than 2 SDs (1.7; solid black horizontal line) above the value for histone H2B were considered to be members of the secretome. Mean Ln transformed ratios of protein abundance (Cm/CA) where identities lying above the black line are actively secreted, and values falling below the dotted line are likely present due to apoptosis or lysis. X-axis numbers correspond to each protein identity, with 358 in total. The mean and SD from at least three measurements for each protein are shown.
Silverman et al. Genome Biology 2008 9:R35 doi:10.1186/gb-2008-9-2-r35