PXD057951-1

PXD057951 is an original dataset announced via ProteomeXchange.

Title	Temperature and Time-Dependent Stability Assessment of Mice Tissue Proteins Using Label-Free Quantitative Proteomics by Mass Spectrometry
Description	Protein biomarkers in disease conditions offer crucial insights into prognosis and treatment options. In research, where protein samples are frequently stored at -20°C and -80°C for extended periods, assessing protein stability under these conditions is essential. We assessed the stability of proteins in both healthy and diseased mice liver tissues stored at 4°C, -20°C, and -80°C for 0, 7, 30, 90, and 180 days. A significant decrease in protein concentrations (over 10% by day 90, p < 0.001) was observed across all storage conditions in the initial BCA assay Further, we conducted an untargeted proteomics analysis using an in-solution trypsin digestion. Raw data generated via LC-Q-Orbitrap-MS/MS and processed with proteome discoverer 2.5. Significant protein groups were identified based on the presence of ≥ 2 unique peptides, a false discovery rate (FDR) of < 1%, and an abundance ratio p-value of ≤ 0.001. Differentially expressed proteins were filtered by p-value and fold change (log2 FC ±2, p-adj ≤ 0.05). Complete degradation was observed in 24, 11, and 8 proteins in healthy samples, and 8, 2, and 3 proteins in diseased samples at 4°C, -20°C, and -80°C, respectively, after 7 days. Notably, 18 of these unstable proteins are previously reported as key biomarkers in disease conditions. Total number of significant proteins consistently identified across all time points in healthy samples was 2570, 2711, and 2617, and in diseased samples was 2124, 2414, and 2353 at 4°C, -20°C, and -80°C, respectively. While -20°C and -80°C provide better conditions for long-term storage, fluctuations in total protein count highlight some instability across storage durations. Therefore, Immediate analysis is preferable to prevent temperature-related protein degradation.
HostingRepository	PRIDE
AnnounceDate	2025-07-02
AnnouncementXML	Submission_2025-07-01_22:59:43.601.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD057951
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	RAMALINGAM PERAMAN
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-15 15:59:40	ID requested
⏵ 1	2025-07-01 22:59:44	announced

10.6019/PXD057951;

submitter keyword: Tissue Proteins

Protein stability

Disease biomarkers

Mass spectrometry

Proteomic Analysis

Ramalingam Peraman
contact affiliation	Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Hajipur, 844102, India
contact email	drramalingamp@gmail.com
lab head
RAMALINGAM PERAMAN
contact affiliation	National Institute of Pharmaceutical Education and Research, Hajipur
contact email	DRRAMALINGAMP@GMAIL.COM
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD057951
     1. Label: PRIDE project
     2. Name: Temperature and Time-Dependent Stability Assessment of Mice Tissue Proteins Using Label-Free Quantitative Proteomics by Mass Spectrometry