Fig. 6.

TMT experimental design from reporter ion interference analysis: A, 5–5 grouped layout for a 10-plex TMT batch with 2 populations and 5 replicates each. Two channels are being affected by cross population primary and secondary reporter ion interference. B, optimal layout for a 10-plex TMT batch with 2 populations and 5 replicates each, with no cross population primary or secondary reporter ion interference. C, optimal 11-plex configuration for 3 populations with 3 replicates each. By leaving two empty channels, it eliminates cross population reporter ion interference. D, optimal 11-plex configuration for 3 populations with 3 replicates each, with one empty channel and one reference line channel. Only two channels suffer primary and secondary reporter ion interference.