In a recently published manuscript in the journal of Molecular and Cellular Proteomics, researchers from the National Cancer Institutes (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigated the effect of cold ischemia on the proteome of fresh frozen tumors. In determining the effect of cold ischemia, the time between the chilling of a tissue, organ, or body part after its blood supply has been reduced or cut off, investigators collected and extensively analyzed human ovarian tumors and patient-derived human breast cancer xenograft tissues without vascular interruption.
In this deep analysis both the global proteome and phosphoproteome were analyzed at a range of ischemic times from 0 minutes to 1 hour with high-resolution mass spectrometry. Results showed that up to 24% of the phosproteome was effected from ischemia, while the global proteome was unchanged up to 1 hour.
This study sheds light on how researchers should interpret phosphoproteomic analysis of biospecimens that have a range of ischemic times. Often in proteomic studies analysis is performed on samples of convenience, these results encourage researchers to interpret stress kinase pathways with caution when there are unknown cold ischemic times.