Fig. 3.

Statistical analysis of differential protein abundance. A and C, Scatter plot of log₂ of spectral count ratios versus log₂ of summed protein level spectral counts (SpC) comparing replicate samples of either WCL (A) or 20KgP (C) from glucose-grown cells. B and D, The same scatter plots comparing fractions from oleate- and glucose-grown cells. For all scatter plots shown, solid purple curves are the LOWESS smoothing curves defining the upper and lower boundaries of the log₂ ratios from control replicates of either WCL (A and B) or 20KgP fractions (C and D). Note that on each plot the proteins with data points that line up in a straight line and bookend the remaining data points are those that were detected in only one of the two fractions.