Protocol for deep proteomic profiling of formalin-fixed paraffin-embedded specimens using a spectral library-free approach.

ABSTRACT: Formalin-fixed paraffin-embedded (FFPE) samples are valuable archived bio-specimens of individuals and are commonly used in biomedical research. Here, we present a protocol for deep proteomic profiling of FFPE specimens using a spectral library-free approach. We describe steps for FFPE tissue collection, tissue lysis, homogenization, protein lysate cleanup, on-beads digestion, and de-salting. We then detail data acquisition and statistical analysis. This protocol is highly sensitive, reproducible, and applicable for high-throughput proteomic profiling and can be used on various types of specimens.

SUBMITTER: Soni RK 

PROVIDER: S-EPMC10319319 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature