ASAP─Automated Sonication-Free Acid-Assisted Proteomes─from Cells and FFPE Tissues

Georgina D. Barnabas, Verena Goebeler, Janice Tsui, Jonathan W. Bush, Philipp F. Lange*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)3291-3299
Number of pages9
JournalAnalytical Chemistry
Issue number6
StatePublished - 14 Feb 2023
Externally publishedYes


Dive into the research topics of 'ASAP─Automated Sonication-Free Acid-Assisted Proteomes─from Cells and FFPE Tissues'. Together they form a unique fingerprint.

Cite this