PXD060473

PXD060473 is an original dataset announced via ProteomeXchange.

Title	Impact of Single Freeze-Thaw Cycles on Serum Protein Stability: Implications for Clinical Biomarker Validation Using Mass Spectrometry
Description	The validated use of biomarkers for clinical diagnostics and therapy necessitates the availability of a substantial number of high-quality samples, along with a complete set of clinical data. Establishing standards for sample collection, storage, and quality control is essential to reduce the variability of sample quality. This study evaluated the impact of a single freeze-and-thaw (FT) cycle on the quality of liquid nitrogen-stored clinical serum aliquots. This was achieved by data-independent acquisition mass spectrometry (DIA-MS) on a test cohort comprising 25 patients and 99 samples, and a validation cohort comprising 109 patients. Abundance differences of paired samples were assessed by employing biostatistics and bioinformatics approaches, including clustering analyses, linear mixed models, functional annotation, and machine learning. Following the library-free data analysis and implementation of strict data preprocessing, the relative abundance of 213 (pilot study) and 248 (validation study) human serum proteins were analyzed by comparing paired fresh (never frozen) and FT samples. The proteomic data demonstrated high quality and reproducibility. Of 30 target proteins observed in the pilot study, 11 proteins (36.6%) were successfully validated in the validation cohort. These targets exhibited significant changes (q-value <0.05) in measurable protein abundance after one FT cycle. A correlation analysis of the measured protein intensity and storage duration revealed no significant association between the two variables. Of the 11 validated FT-sensitive proteins, CP and IGHV6-1 were identified as potential biomarker candidates for discriminating between malignant and benign pancreatic disease patients. Distinct protein abundance patterns can be discerned between fresh serum samples and samples stored in liquid nitrogen. The findings of this study suggest that FT cycles are important pre-analytical impact factors and should be addressed during the translation of protein-based biomarkers into clinical use.
HostingRepository	PRIDE
AnnounceDate	2026-04-21
AnnouncementXML	Submission_2026-04-21_13:23:57.671.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thorben Sauer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-04 11:34:17	ID requested
⏵ 1	2026-04-21 13:23:58	announced

Dataset with its publication pending

submitter keyword: clinical research, sample storage, DIA-MS,Proteomics, Biobanking, liquid nitrogen, Biomarkers, translation

Prof. Dr.
contact affiliation	Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck
contact email	timo.gemoll@uni-luebeck.de
lab head
Thorben Sauer
contact affiliation	Department of Surgery, Laboratory for Surgical Research, University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538 Lübeck Germany
contact email	thorben.sauer@student.uni-luebeck.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060473
     1. Label: PRIDE project
     2. Name: Impact of Single Freeze-Thaw Cycles on Serum Protein Stability: Implications for Clinical Biomarker Validation Using Mass Spectrometry