Fig. 2 Examples of two inter-experimental normalization methods that can be used for comparison of different
multiplex experiments after intra-experimental normalization. (A) Normalization method based on a reference
channel. A 6-plex experiment can be compared with another 6-plex experiment by the inclusion of a reference
sample or master pool in one of the channels (tag 6 in the example). The intensity of each protein is expressed
as a ratio of the intensity of the same protein in the reference channel. (B) Normalization method based on
channel proportions. The intensity for each protein in each channel is expressed as the proportion of the sum
of intensities for that protein in all channels. As a result, the sum of normalized intensities in all channels for
each protein is 1, as in [40]. The sum of intensities across all proteins should give the same value for all
channels, also as in [40], on the basis of intra-experimental normalization performed before interexperimental normalization. For the sake of simplicity, only two multiplex experiments are included in both
examples although the same procedure could be applied to additional experiments performed under similar
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