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*

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Resumé

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.

OriginalsprogEngelsk
TidsskriftEuPA Open Proteonomics
Vol/bind10
Sider (fra-til)9-18
ISSN2212-9685
DOI
StatusUdgivet - 2016

Fingeraftryk

Proteome
Paraffin
Formaldehyde
Biopsy
Tissue
Proteins
Colon
Stabilization
Throughput

Citer dette

Bennike, Tue Bjerg ; Kastaniegaard, Kenneth ; Padurariu, Simona ; Gaihede, Michael ; Birkelund, Svend ; Andersen, Vibeke ; Stensballe, Allan. / Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples. I: EuPA Open Proteonomics. 2016 ; Bind 10. s. 9-18.
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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.",
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Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples. / Bennike, Tue Bjerg; Kastaniegaard, Kenneth; Padurariu, Simona; Gaihede, Michael; Birkelund, Svend; Andersen, Vibeke; Stensballe, Allan.

I: EuPA Open Proteonomics, Bind 10, 2016, s. 9-18.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

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 - Formalin-fixed

KW - Human colon mucosa

KW - Mass spectrometry

KW - Paraffin-embedded

KW - Preservation

KW - Proteomics

KW - RNAlater

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 -