posted on 2023-02-01, 17:35authored byGeorgina
D. Barnabas, Verena Goebeler, Janice Tsui, Jonathan W. Bush, Philipp F. Lange
Formalin-fixed, paraffin-embedded (FFPE) tissues are
an invaluable
resource for retrospective studies, but protein extraction and subsequent
sample processing steps have been shown to be challenging for mass
spectrometry (MS) analysis. Streamlined high-throughput sample preparation
workflows are essential for efficient peptide extraction from complex
clinical specimens such as fresh frozen tissues or FFPE. Overall,
proteome analysis has gained significant improvements in the instrumentation,
acquisition methods, sample preparation workflows, and analysis pipelines,
yet even the most recent FFPE workflows remain complex and are not
readily scalable. Here, we present an optimized workflow for automated
sonication-free acid-assisted proteome (ASAP) extraction from FFPE
sections. ASAP enables efficient protein extraction from FFPE specimens,
achieving similar proteome coverage as established methods using expensive
sonicators, resulting in reduced sample processing time. The broad
applicability of ASAP on archived pediatric tumor FFPE specimens resulted
in high-quality data with increased proteome coverage and quantitative
reproducibility. Our study demonstrates the practicality and superiority
of the ASAP workflow as a streamlined, time- and cost-effective pipeline
for high-throughput FFPE proteomics of clinical specimens.