A 3-digit binary code (A) was used to encode the availability for the three unexposed experiment set (B) and the three exposed experiment set (C). The data obtained from the two sets were then used to determine the agreement of availability of raw spectra data for all the six replicates. Of the total 1634 protein spots analyzed, 94.4% unexposed set and 91.4% in exposed set had presence of spectra in all replicates. In the case of the 173 differentially abundant proteins, there was presence of spectra in all the unexposed experiments while in two protein spots no spectra were detected. The probability that this distribution of presence/absence for the differentially abundant proteins was due to chance was tested using the Sign test. The probability was less than 0.0001.
