Scalable Acid-Aided Lysis of Skin Samples Improves Proteome Coverage

In this study, we present a robust and scalable sample preparation protocol based on chemical lysis with trifluoroacetic acid (TFA), adapted from the SPEED method and optimized for human skin samples. The protocol simplifies tissue lysis while selectively leaving ECM scaffolds largely insoluble. As a result, abundant collagens and structural proteins are effectively depleted from the soluble fraction, improving the dynamic range of detectable proteins and increasing sensitivity for less abundant species. Using TFA lysis followed by solid-phase-enhanced sample preparation (SP3), we identified up to 6,200 protein groups from full-thickness human skin punch biopsies. Notably, the protocol enables high-depth proteomic analysis from 2 mm punch biopsies, which are less invasive and more suitable for longitudinal or large-cohort studies. Tape strip samples—commonly used in dermatological research for minimally invasive epidermal sampling—were also compatible with this protocol, yielding up to 2,300 protein groups, representing a two- to threefold increase compared to previously reported studies.