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Resources for working with FFPE tissue samples
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Cell lines
Model organisms
Plant tissues
Biological fluids
Immunoprecipitations
Mammalian tissues
FFPE tissues
FFPE tissues
Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable resource for a variety of clinical samples. Unlike fresh or frozen tissue samples, FFPE samples can be stored at room temperature for extended periods and therefore, are cost-effective for long-term storage since freezer space is not needed. Consequently, clinical FFPE specimens are routinely collected and stored in large libraries with extensive information on clinical metadata.
FFPE samples provide valuable resources for mass spectrometry (MS)-based proteomics studies for identifying potential disease biomarkers, monitoring proteomic changes associated with disease progression, and therapeutic drug response.
However, despite the huge potential, FFPE samples are not routinely analyzed by MS due to challenges associated with the nature of sample preservation. Harsh conditions are required to reverse protein cross-links to access proteins and to remove the paraffin embedding. Traditional workflows often include a time-consuming xylene-based deparaffinization step that poses a health hazard due to high toxicity and results in low reproducibility with the risk of sample loss. Therefore, traditional FFPE workflows are technically demanding and involve many manual steps rendering them unsuitable for the analysis of large cohorts.
PreOmics®’ novel FFPE protocol combines the BeatBox Tissue Homogenizer and iST sample preparation technology to simplify, speed up, and standardize FFPE sample preparation. The optimized protocol avoids the sample deparaffinization step and is xylene free. The workflow is scalable and enables fast and robust processing of up to 96 samples in parallel from starting material to clean peptides within one working day.
Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable resource for a variety of clinical samples. Unlike fresh or frozen tissue samples, FFPE samples can be stored at room temperature for extended periods and therefore, are cost-effective for long-term storage since freezer space is not needed. Consequently, clinical FFPE specimens are routinely collected and stored in large libraries with extensive information on clinical metadata.
FFPE samples provide valuable resources for mass spectrometry (MS)-based proteomics studies for identifying potential disease biomarkers, monitoring proteomic changes associated with disease progression, and therapeutic drug response.
However, despite the huge potential, FFPE samples are not routinely analyzed by MS due to challenges associated with the nature of sample preservation. Harsh conditions are required to reverse protein cross-links to access proteins and to remove the paraffin embedding. Traditional workflows often include a time-consuming xylene-based deparaffinization step that poses a health hazard due to high toxicity and results in low reproducibility with the risk of sample loss. Therefore, traditional FFPE workflows are technically demanding and involve many manual steps rendering them unsuitable for the analysis of large cohorts.
PreOmics®’ novel FFPE protocol combines the BeatBox Tissue Homogenizer and iST sample preparation technology to simplify, speed up, and standardize FFPE sample preparation. The optimized protocol avoids the sample deparaffinization step and is xylene free. The workflow is scalable and enables fast and robust processing of up to 96 samples in parallel from starting material to clean peptides within one working day.
