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Updated: Jul 13, 2026

Extraction of Tissue Antigens for Functional Assays
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A Standard Operating Procedure for Protein Extraction From Abdominal Aortic Aneurysm Tissue: Enhancing Proteomics

Telmo Baltazar1, Fábio Trindade1, Rita Nogueira-Ferreira1

  • 1RISE-Health, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, Porto, Portugal.

Proteomics. Clinical Applications
|November 14, 2025
PubMed
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This study optimized a protein extraction protocol for abdominal aortic aneurysm (AAA) tissue, improving biomarker discovery. The developed standard operating procedure (SOP) enhances reproducibility for AAA proteomic analysis.

Area of Science:

  • Proteomics
  • Biomarker Discovery
  • Vascular Medicine

Background:

  • Abdominal aortic aneurysm (AAA) is a poorly understood disease lacking effective treatments beyond surgery.
  • Identifying biomarkers is crucial for early diagnosis and understanding AAA pathophysiology.
  • Tissue heterogeneity in AAA poses challenges for reproducible proteomic analysis.

Purpose of the Study:

  • To optimize a protein extraction protocol for AAA tissue to maximize protein yield.
  • To develop a Standard Operating Procedure (SOP) for reproducible AAA tissue homogenization and protein extraction.
  • To facilitate the translation of proteomics findings into clinical diagnostic and prognostic tools.

Main Methods:

  • Compared bead size, homogenization cycles, bead-to-tissue ratio, lysis buffer volume, and chemistry for protein extraction efficiency.
Keywords:
SOPabdominal aortic aneurysmaortic tissue homogenizationprotein extractionproteomics

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  • Utilized a bead-beating homogenization method for AAA tissue processing.
  • Applied bioinformatic analysis to identify key AAA pathogenesis-related pathways from extracted proteomes.

    • Main Results:

    • Optimal protein extraction achieved with 1.4 mm beads, two cycles, a 30:1 bead-to-tissue ratio, and 20 µL lysis buffer per mg tissue.
    • RIPA buffer yielded greater sequence coverage, while HEPES and Urea/thiourea buffers were preferred for quantification.
    • The developed SOP successfully characterized the AAA tissue proteome, highlighting relevant pathways.

    Conclusions:

    • The optimized SOP is effective for identifying and quantifying proteins in AAA tissue.
    • This standardized protocol can accelerate the development of clinical diagnostic and prognostic tools for AAA.
    • Improved reproducibility in AAA proteomics will bolster the translation of research findings into clinical practice.