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Figure S1. Skin tissue-related application platform of MELC robot technology. The MELC core process of repeated cycling of antibody/tag incubation, fluorescence imaging and photo bleaching provides a series of fluorescence images (left image stack of the flow diagram). The process may be continued up to a maximum marker number of at least n = 100. A basic mode of postprocessing involves r(ed)/g(reen)/b(lue) imaging directed to three selected, correspondingly coloured markers (left part of the illustration). An advanced mode of postprocessing comprises binarization of fluorescence images under i) expert supervision and ii) consideration of anatomical horizontal orientation of the basal membrane zone (right image stack). This is the precondition for analysis of the expression of single epitopes or combinatorial molecular phenotypes (CMP) in a given dimension (i.e. pixel events normalized, PEN, in relation to 100 μm horizontal skin width). This allows a subsequent rigorous statistical comparison of topoproteome information in appropriate cohorts by means of a so-called topominer strategy (right part of the illustration).

Table S1. Single epitope expression in APT and NPT lesions. PEN (pixel events normalised in relation to 100 μm horizontal skin width) as a mean of APT (n = 6) and NPT (n = 6) patients ± SD and the p-value. EfaBS = Efalizumab Binding Site.

Table S2. Combinatorial molecular phenotype (CMP) motifs with significant differences between APT and NPT lesions. Relative expression in PEN (pixel events normalised, mean ± SD for n = 6 patients with APT and NPT each).

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