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.
Keywords: CAN, acetonitrile; DF, directly-frozen; FA, formic acid; FASP, filter-aided sample preparation; FDR, false discovery rate; FFPE, formalin-fixed; Formalin-fixed; HLA-A class I, histocompatibility antigen A-23 alpha chain; HLA-DRB1 class II, histocompatibility antigen DRB1-4 beta chain; Human colon mucosa; LFQ, label-free quantification; Mass spectrometry; PCA, principle component analysis; PSM, peptide spectral match; PTM, post-translational modification; Paraffin-embedded; Preservation; Proteomics; RNAlater; SDC, sodium deoxycholate; SDS, sodium dodecyl sulfate; TEAB, triethylammonium bicarbonate; iFFPE, immediately formalin-fixed; s, standard deviation; sFFPE, stored for 30 min prior to formalin-fixed.