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PXD030367 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePreserving the phosphoproteome of clinical biopsies using a quick freeze collection device
DescriptionThe current gold standard for collecting and processing cancer biopsies is to flash freeze tumor samples in liquid nitrogen. However, in many clinical settings liquid nitrogen is not readily available, and neither the personnel nor the infrastructure is generally available to rapidly process the tumor samples. As a result, tumors are often subjected to prolonged ischemia and/or chemical fixatives, altering the phosphoproteome such that it may no longer reflect the true in vivo state of the tumor. There is a need for an economical, single-use device that can be stored at room temperature then activated at point of care to rapidly freeze the specimen. Our proof-of-concept quick-freeze prototype device focused on key requirements including cooling performance, device safety, minimizing use error, and the ability to ship via existing cold chain logistics. We have demonstrated that our device can cool a core sample below 0°C in less than 70 seconds, below -8°C in less than 150 seconds, and maintain that sample below 0°C for greater than 70 minutes. To demonstrate feasibility, the performance of our prototype was benchmarked against flash freezing in liquid nitrogen using melanoma-bearing PDX mice as a model system. After subjecting the mice to total body irradiation to elicit a phosphosignaling response in the DNA damage response pathway, tumors were harvested and quadrisected with two parts of the tumor snap frozen in liquid nitrogen, and the remaining two parts rapidly cooled in the prototype quick-freeze biospecimen containers for 1 hour. Phosphoproteins were profiled by LC-MS/MS. The prototype freeze device showed feasibility with bias within acceptable limits and slightly higher variability for a subset of phosphopeptides compared to flash freezing. The prototype device forms the framework for development of a commercial device that will improve tissue biopsy preservation for measurement of important phospho-signaling molecules.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterJacob Kennedy
SpeciesList scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationListPhospho; Label:13C(6)15N(2); Label:13C(6)15N(4); Label:13C(6)15N(1); Carbamidomethyl
InstrumentQTRAP 5500
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-12-13 07:51:28ID requested
12022-07-18 15:11:58announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Phosphoproteome, PDX, tumor, tissue, frozen, IMAC, targeted mass spectrometry, immuno-MRM, immunopeptide enrichment, multiple reaction monitoring
Contact List
Jeff Whiteaker
contact affiliationFred Hutchinson Cancer Research Center
contact emailjwhiteak@fhcrc.org
lab head
Jacob Kennedy
contact affiliationFred Hutchinson Cancer Research Center
contact emailjkennedy@fhcrc.org
dataset submitter
Full Dataset Link List
Panorama Public dataset URI