title: Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies.
abstract: Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control ("Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples" [1]). We here report the data from the analysis. The comparative analysis was performed on 24 colon mucosa biopsies, extracted from the sigmoideum of two gastroenterologically healthy participants for the purpose of this study. A set of biopsies were additionally stored for 30 min at room temperature prior to formalin-fixation. The samples were analyzed by high throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002029.
authors.affiliation: Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark; Department of Health Science and Technology, Aalborg University, Aalborg, Denmark.
authors.forename: Tue Bjerg
authors.initials: TB
authors.lastname: Bennike
authors.affiliation: Department of Health Science and Technology, Aalborg University, Aalborg, Denmark.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Kastaniegaard
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark.
authors.forename: Simona
authors.initials: S
authors.lastname: Padurariu
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Michael
authors.initials: M
authors.lastname: Gaihede
authors.affiliation: Department of Health Science and Technology, Aalborg University, Aalborg, Denmark.
authors.forename: Svend
authors.initials: S
authors.lastname: Birkelund
authors.affiliation: Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark; Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark.
authors.forename: Vibeke
authors.initials: V
authors.lastname: Andersen
authors.affiliation: Department of Health Science and Technology, Aalborg University, Aalborg, Denmark.
authors.forename: Allan
authors.initials: A
authors.lastname: Stensballe
keywords: Colon; FFPE; Human; LC–MS; Mucosa; Proteomics; RNAlater; Snap-frozen; Stability