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Abstract

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.
Original languageEnglish
JournalEuPA Open Proteomics
Volume10
Pages (from-to)9-18
ISSN2212-9685
DOIs
Publication statusPublished - 2016

Fingerprint

Proteome
Paraffin
Formaldehyde
Biopsy
Tissue
Tissue Preservation
Proteins
Proteomics
Colon
Stabilization
Throughput

Keywords

  • proteomics
  • RNAlater
  • paraffin-embedded
  • human colon mucosa
  • preservation
  • mass spectrometry

Cite this

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title = "Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples",
abstract = "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 = "proteomics, RNAlater, paraffin-embedded, human colon mucosa, preservation, mass spectrometry",
author = "Bennike, {Tue Bjerg} and Kenneth Kastaniegaard and Simona Padurariu and Michael Gaihede and Svend Birkelund and Vibeke Andersen and Allan Stensballe",
year = "2016",
doi = "10.1016/j.euprot.2015.10.001",
language = "English",
volume = "10",
pages = "9--18",
journal = "EuPA Open Proteonomics",
issn = "2212-9685",
publisher = "Elsevier",

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TY - JOUR

T1 - Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples

AU - Bennike, Tue Bjerg

AU - Kastaniegaard, Kenneth

AU - Padurariu, Simona

AU - Gaihede, Michael

AU - Birkelund, Svend

AU - Andersen, Vibeke

AU - Stensballe, Allan

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - proteomics

KW - RNAlater

KW - paraffin-embedded

KW - human colon mucosa

KW - preservation

KW - mass spectrometry

U2 - 10.1016/j.euprot.2015.10.001

DO - 10.1016/j.euprot.2015.10.001

M3 - Journal article

VL - 10

SP - 9

EP - 18

JO - EuPA Open Proteonomics

JF - EuPA Open Proteonomics

SN - 2212-9685

ER -