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

Tue Bjerg Bennike; Kenneth Kastaniegaard; Simona  Padurariu; Michael Gaihede; Svend Birkelund; Vibeke Andersen; Allan Stensballe

doi:10.1016/j.euprot.2015.10.001

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

Tue Bjerg Bennike, Kenneth Kastaniegaard, Simona Padurariu, Michael Gaihede, Svend Birkelund, Vibeke Andersen, Allan Stensballe

Research output: Contribution to journal › Journal article › Research › peer-review

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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 language	English
Journal	EuPA Open Proteomics
Volume	10
Pages (from-to)	9-18
ISSN	2212-9685
DOIs	https://doi.org/10.1016/j.euprot.2015.10.001
Publication status	Published - 2016

Keywords

proteomics
RNAlater
paraffin-embedded
human colon mucosa
preservation
mass spectrometry

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10.1016/j.euprot.2015.10.001Licence: CC BY-NC-ND 4.0

Open Access articleFinal published version, 1.17 MBLicence: CC BY-NC-ND 4.0

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Optimizing protein analysis by mass spectrometry technology
Bennike, T. B.
01/01/2013 → 31/12/2019
Project: Research

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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",

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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

SN - 2212-9685

VL - 10

SP - 9

EP - 18

JO - EuPA Open Proteomics

JF - EuPA Open Proteomics

ER -

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

Abstract

Keywords

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Optimizing protein analysis by mass spectrometry technology

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