Tape-Stripped Proteomics: A Comparative Analysis of Different Sample Collection Approaches

Tape-stripping of the stratum corneum is a promising non-invasive approach for proteomic analysis of skin lesions, but the effects of sampling design and disc pressure on proteome readout remain poorly defined. Here, we assessed how inclusion of surrounding normal-looking skin and variation in adhesive disc pressure influence protein detection from small melanocytic lesions. D-squame tape strips were collected from six participants, including three moles and one matched normal skin site per participant. For lesion 1 (L1), discs were applied using light finger pressure. For lesion 2 (L2), the mole area was marked on the disc and separated from the surrounding skin, which was analysed separately (L2S). For lesion 3 (L3), increased pressure was applied using the upper barrel tip of a marker before excising the lesion-matched area. Samples were analysed by DIA-MS with DIA-NN processing. In total, 2882 protein groups were identified, including 1719 shared across all groups. L3 yielded the highest number of unique proteins (77) and significantly altered proteins versus normal skin (142), compared with L2 (54 unique; 52 altered), L1 (30 unique; 4 altered), L2S (16 unique; 3 altered), and normal skin (7 unique). These findings show that precise lesion-matched disc trimming and increased application pressure substantially improve tape-strip proteomic depth and lesion-specific signal detection. Multivariate analysis and supervised classification further separated lesional samples-most clearly the pressure-assisted L3-from other collection methods, supporting these observations, although the small cohort warrants cautious interpretation.