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<p>Clinical proteomics has the potential to add a valuable data layer to genomic and histopathological analyses in precision oncology, but its application to limited clinical material remains challenging. Here, we demonstrate that state-of-the-art mass spectrometry-based proteomics enables in-depth proteomic profiling of formalin-fixed paraffin-embedded (FFPE) clinical samples, including small diagnostic biopsies and single tissue sections mounted on glass slides. Despite minimal input material, single-slide analyses of clinical lung tumor specimens yielded biologically and clinically informative data, supporting detection of actionable proteins, immune-related signatures, and multivariate biomarkers. These results establish the feasibility of proteomics for retrospective FFPE studies and routine clinical practice, expanding opportunities for biomarker discovery and precision medicine from scarce tissue material.</p>

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Mass spectrometry-based proteomics delivers in-depth proteome profiling of FFPE lung cancer biopsies from single glass slides

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月29日

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  • Olena Berkovska,
  • Igor Schliemann,
  • Georgios Mermelekas,
  • Nazlı Ezgi Özkan,
  • Mahnaz Nikpour,
  • Vilde Drageset Haakensen,
  • Åslaug Helland,
  • Janne Lehtiö,
  • Lukas M. Orre

摘要

Clinical proteomics has the potential to add a valuable data layer to genomic and histopathological analyses in precision oncology, but its application to limited clinical material remains challenging. Here, we demonstrate that state-of-the-art mass spectrometry-based proteomics enables in-depth proteomic profiling of formalin-fixed paraffin-embedded (FFPE) clinical samples, including small diagnostic biopsies and single tissue sections mounted on glass slides. Despite minimal input material, single-slide analyses of clinical lung tumor specimens yielded biologically and clinically informative data, supporting detection of actionable proteins, immune-related signatures, and multivariate biomarkers. These results establish the feasibility of proteomics for retrospective FFPE studies and routine clinical practice, expanding opportunities for biomarker discovery and precision medicine from scarce tissue material.