Scalable Acid-Aided Lysis of Skin Samples Improves Proteome Coverage

Area of Science:

• Proteomics
• Dermatology
• Biochemistry

Background:

• Liquid chromatography-mass spectrometry (LC-MS) is crucial for tissue proteomic analysis.
• Analyzing full-thickness human skin is challenging due to extensive extracellular matrix (ECM) crosslinking and high-abundance ECM proteins.
• These limitations in skin proteomics hinder comprehensive analysis and discovery.

Purpose of the Study:

• To adapt and validate the Trifluoroacetic acid (TFA)-based SPEED method for enhanced skin proteomic analysis.
• To improve protein extraction efficiency and increase proteome coverage in human skin samples.
• To enable sensitive analysis from minimally invasive skin biopsies.

Main Methods:

• Adapted the Trifluoroacetic acid (TFA)-based SPEED method for human skin samples.
• Utilized TFA to remove abundant crosslinked ECM proteins without disrupting most crosslinks.
• Applied the method to both full-thickness skin biopsies and tape strip samples.

Main Results:

• Achieved identification of over 6,200 protein groups in healthy human skin.
• Enabled analysis of minimally invasive 2 mm punch biopsies, increasing potential patient enrollment.
• Identified up to 2,300 proteins in healthy skin using tape strip proteomics, offering a cost-effective alternative.

Conclusions:

• The adapted SPEED method significantly enhances proteome coverage and protein identification in human skin.
• This approach facilitates sensitive analysis from small, minimally invasive biopsies, advancing skin proteomics research.
• The method provides a scalable and cost-effective solution for skin and tape strip proteomics, supporting future applications like machine learning.