Abstract
We describe a novel antigen-retrieval method using a micro-sized chamber for mass spectrometry (MS) analysis to identify proteins that are preferentially eluted from formalin-fixed paraffin-embedded (FFPE) samples. This approach revealed that heat-induced antigen retrieval (HIAR) from an FFPE sample fixed on a glass slide not only improves protein identification, but also facilitates preferential elution of protein subsets corresponding to the properties of antigen-retrieval buffers. Our approach may contribute to an understanding of the mechanism of HIAR.
Highlights
The standard method for storing clinical specimens in hospital tissue banks is in the form of formalin-fixed paraffin-embedded (FFPE) tissue samples, and these are both abundant and widely available for pathological diagnosis worldwide
Evaluation of heat-induced antigen retrieval (HIAR) using micro-sized chamber To evaluate the feasibility of HIAR using the microsized chamber, we compared the number of identified proteins under each sample condition (Figure 3A)
These results suggested that protein identification was not influenced by the size of the chamber used for antigen retrieval
Summary
The standard method for storing clinical specimens in hospital tissue banks is in the form of formalin-fixed paraffin-embedded (FFPE) tissue samples, and these are both abundant and widely available for pathological diagnosis worldwide. FFPE tissue samples have been subjected to mass spectrometry (MS)-based proteomic analysis [1,2,3,4], and several studies in FFPE samples employed heat-induced antigen retrieval (HIAR) to improve protein identification [1,4,5,6,7,8,9,10,11,12] These investigations have demonstrated the similarity of protein identification between FFPE and fresh/frozen tissue samples [4,9,12,13,14,15]. The proteins released from FFPE samples by HIAR were not investigated or characterized by MS analysis
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