Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples

•We evaluated proteome analyses of snap frozen, RNAlater, and FFPE preserved samples.•Reliable proteome studies can be conducted on RNAlater, and FFPE preserved samples.•RNAlater sample preservation is highly usable for proteomics studies.

Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described.Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30 min. The protein content of the samples was characterized by high throughput quantitative proteomics.We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.

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