Summary plots of the peptidome of Q7Q7, Q7Q111 and Q111Q111 cells.

<p>The relative levels of all peptides identified by MS/MS analysis in the Q7Q111 (A) and Q111Q111 (B) cells were compared to the average level of the peptide in Q7Q7 cells. The <i>y</i>-axis represents relative peptide levels (log-scale) and the <i>x</i>-axis represents the rank order of peptides sorted according to the relative level. For those peptides detected multiple times (different charge states and/or tag numbers), the relative ratio for each form was considered separately. If the ratio was <0.20, the value was capped at 0.20 to reflect the typical signal to noise ratio. The red circles represent the ratio of each replicate of the identified peptides in Q7Q111 or Q111Q111 cells, expressed relative to the level in Q7Q7 cells for that LC-MS run. The black circles represent the ratio of each Q7Q7 replicate expressed relative to the average level of Q7Q7 replicates in that LC-MS run (i.e. run 1 and 2; the other two runs did not include replicates of Q7Q7 cells).