Impact of temperature dependent sampling procedures in proteomics and peptidomics--a characterization of the liver and pancreas post mortem degradome.
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 nonneural 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 min post mortem time) mouse liver and pancreas tissue is compared with rapid heat stabilization with regard to effects on the proteome (using two-dimensional differential in-gel electrophoresis) and peptidome (using label free liquid chromatography). We report several 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.
Scholz
Birger
B
Department of Pharmaceutical Biosciences, Division of Toxicology, BMC, Box 594, SE-75124 Uppsala University, and Department of Medical Sciences, Clinical Pharmacology, Uppsala University Hospital, Uppsala, Sweden.
Sköld
Karl
K
Kultima
Kim
K
Fernandez
Celine
C
Waldemarson
Sofia
S
Savitski
Mikhail M
MM
Söderquist
Marcus
M
Borén
Mats
M
Stella
Robert
R
Andrén
Per
P
Zubarev
Roman
R
James
Peter
P
D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D007328:Insulin / Q000737:chemistry / Q000378:metabolism; D008099:Liver / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D010179:Pancreas / Q000378:metabolism*; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D011180:Postmortem Changes; D020033:Protein Isoforms / Q000737:chemistry / Q000378:metabolism; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D013696:Temperature
D007328:Insulin; D019151:Peptide Library; D010455:Peptides; D020033:Protein Isoforms; D020543:Proteome