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Impact of temperature dependent sampling procedures in proteomics and peptidomics – A characterization of the liver and pancreas post mortem degradome

Schultz, Birger; Sköld, Karl; Kultima, Kim; Fernandez, Celine LU ; Waldemarson, Sofia LU ; Savitski, Mikhail; Svensson, Marcus; Borén, Mats; Stella, Roberto and Andrén, Per, et al. (2011) In Molecular & Cellular Proteomics 10(3).
Abstract
Little is known about the nature of post mortem degradation of proteins and peptides on a global level, the so-called degradome. This is especially true for non-neural tissues. Degradome properties in relation to sampling procedures on different tissues are of great importance for the studies of for instance post translational modifications and/or the establishment of clinical biobanks. Here, snap freezing of fresh (< 2 minutes post mortem time) mouse liver and pancreas tissue is compared to rapid heat stabilization with regard to effects on the proteome (using 2D-DIGE) and peptidome (using label free LC-MS). We report a number of proteins and peptides that exhibit heightened degradation sensitivity, for instance superoxide dismutase in... (More)
Little is known about the nature of post mortem degradation of proteins and peptides on a global level, the so-called degradome. This is especially true for non-neural tissues. Degradome properties in relation to sampling procedures on different tissues are of great importance for the studies of for instance post translational modifications and/or the establishment of clinical biobanks. Here, snap freezing of fresh (< 2 minutes post mortem time) mouse liver and pancreas tissue is compared to rapid heat stabilization with regard to effects on the proteome (using 2D-DIGE) and peptidome (using label free LC-MS). We report a number of proteins and peptides that exhibit heightened degradation sensitivity, for instance superoxide dismutase in liver, and peptidyl-prolyl cis-trans isomerase and insulin C-peptides in pancreas. Tissue sampling based on snap freezing produces a greater amount of degradation products and lower levels of endogenous peptides than rapid heat stabilization. We also demonstrate that solely snap freezing related degradation can be attenuated by subsequent heat stabilization. We conclude that tissue sampling involving a rapid heat stabilization step is preferable to freezing with regard to proteomic and peptidomic sample quality. (Less)
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published
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Molecular & Cellular Proteomics
volume
10
issue
3
publisher
American Society for Biochemistry and Molecular Biology
external identifiers
  • wos:000287847200027
  • scopus:77956298568
ISSN
1535-9484
DOI
10.1074/mcp.M900229-MCP200
language
English
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yes
id
0b3eabcb-558e-49d3-af8a-78133f6b1f50 (old id 1658682)
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2010-08-23 09:54:58
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2017-11-05 03:18:10
@article{0b3eabcb-558e-49d3-af8a-78133f6b1f50,
  abstract     = {Little is known about the nature of post mortem degradation of proteins and peptides on a global level, the so-called degradome. This is especially true for non-neural tissues. Degradome properties in relation to sampling procedures on different tissues are of great importance for the studies of for instance post translational modifications and/or the establishment of clinical biobanks. Here, snap freezing of fresh (&lt; 2 minutes post mortem time) mouse liver and pancreas tissue is compared to rapid heat stabilization with regard to effects on the proteome (using 2D-DIGE) and peptidome (using label free LC-MS). We report a number of proteins and peptides that exhibit heightened degradation sensitivity, for instance superoxide dismutase in liver, and peptidyl-prolyl cis-trans isomerase and insulin C-peptides in pancreas. Tissue sampling based on snap freezing produces a greater amount of degradation products and lower levels of endogenous peptides than rapid heat stabilization. We also demonstrate that solely snap freezing related degradation can be attenuated by subsequent heat stabilization. We conclude that tissue sampling involving a rapid heat stabilization step is preferable to freezing with regard to proteomic and peptidomic sample quality.},
  author       = {Schultz, Birger and Sköld, Karl and Kultima, Kim and Fernandez, Celine and Waldemarson, Sofia and Savitski, Mikhail and Svensson, Marcus and Borén, Mats and Stella, Roberto and Andrén, Per and Zubarev, Roman and James, Peter},
  issn         = {1535-9484},
  language     = {eng},
  number       = {3},
  publisher    = {American Society for Biochemistry and Molecular Biology},
  series       = {Molecular & Cellular Proteomics},
  title        = {Impact of temperature dependent sampling procedures in proteomics and peptidomics – A characterization of the liver and pancreas post mortem degradome},
  url          = {http://dx.doi.org/10.1074/mcp.M900229-MCP200},
  volume       = {10},
  year         = {2011},
}