title: Impact of temperature dependent sampling procedures in proteomics and peptidomics--a characterization of the liver and pancreas post mortem degradome.
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 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.
authors.affiliation: 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.
authors.forename: Birger
authors.initials: B
authors.lastname: Scholz
authors.forename: Karl
authors.initials: K
authors.lastname: Sköld
authors.forename: Kim
authors.initials: K
authors.lastname: Kultima
authors.forename: Celine
authors.initials: C
authors.lastname: Fernandez
authors.forename: Sofia
authors.initials: S
authors.lastname: Waldemarson
authors.forename: Mikhail M
authors.initials: MM
authors.lastname: Savitski
authors.forename: Marcus
authors.initials: M
authors.lastname: Söderquist
authors.forename: Mats
authors.initials: M
authors.lastname: Borén
authors.forename: Robert
authors.initials: R
authors.lastname: Stella
authors.forename: Per
authors.initials: P
authors.lastname: Andrén
authors.forename: Roman
authors.initials: R
authors.lastname: Zubarev
authors.forename: Peter
authors.initials: P
authors.lastname: James
mesh_terms: 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
chemical_list: D007328:Insulin; D019151:Peptide Library; D010455:Peptides; D020033:Protein Isoforms; D020543:Proteome