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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 Jun

REPOSITORIES: biostudies-literature

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

Soni Rajesh Kumar RK

STAR protocols 20230624 3

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, reproducibl ...[more]

PMID: 37355991

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