PXD066741

PXD066741 is an original dataset announced via ProteomeXchange.

Title	The impact of long-term cryopreservation on serum proteomic and trace metal integrity in biobanking
Description	Background: Long-term cryopreservation compromises biobank sample integrity, yet systematic studies on its impact on serum proteomic and trace metal profiles remain scarce, hindering reliable biomarker research. Methods: We employed inductively coupled plasma mass spectrometry (ICP-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) with data-independent acquisition (DIA) to analyze serum samples from healthy donors after short-term (1 year) versus long-term (6 years) cryopreservation. Analyses included protein integrity assessment (SDS-PAGE), quantitative proteomics, trace metal quantification (10 elements), and functional enrichment (GO, KEGG). Results: Long-term cryopreservation induced substantial molecular alterations: SDS-PAGE revealed degradation of high-molecular-weight proteins (>100 kDa) and accumulation of low-molecular-weight fragments (<35 kDa). Proteomic analysis identified 242 significantly altered proteins (176 up-regulated, 66 down-regulated), enriched in immune response, metabolic pathways, and extracellular matrix organization. Paradoxically, long-term samples exhibited superior LC-MS/MS technical performance (lower CV: 22.9% vs 26.3%; fewer missing values: 15% vs 29%) attributed to artifacts arising from sample degradation. ICP-MS revealed significant concentration changes for V, Mn, Fe, Zn, Rb, and Cs. Conclusions: Our integrated analysis demonstrates that prolonged cryopreservation compromises serum molecular integrity through protein degradation/aggregation, biological pathway dysregulation, and trace metal redistribution. Crucially, apparent improvements in LC-MS/MS data quality are degradation artifacts, challenging conventional quality metrics.
HostingRepository	iProX
AnnounceDate	2025-07-30
AnnouncementXML	Submission_2025-07-29_20:20:09.035.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xiongshun Liang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-29 20:12:39	ID requested
⏵ 1	2025-07-29 20:20:09	announced

Dataset with its publication pending

submitter keyword: Serum, Long-term cryopreservation, Proteomics, Trace metal, quality control, Biobanks

Wenxu Hong
contact affiliation	Shenzhen Center for Chronic Disease Control
contact email	liangxiongshun@163.com
lab head
Xiongshun Liang
contact affiliation	Shenzhen Center for Chronic Disease Control and Prevention
contact email	675627664@qq.com
dataset submitter

iProX dataset URI