SWIFT Proteomic Data from Mouse Organs for FF and FFPE Tissue Analysis

Up to ∼10,000 protein groups and ∼150,000 peptides were identified across multiple mouse organs using the timsTOF Pro mass spectrometer. The dataset, created by Chuping Wei and last updated in April 2026, supports the SWIFT workflow for efficient proteomic preparation of fresh-frozen and formalin-fixed paraffin-embedded tissues. It demonstrates high repeatability with pairwise Pearson’s r > 0.96 across six experimental replicates and a dynamic range spanning 6–7 orders of magnitude.

Use Cases

• Benchmarking proteomic workflow efficiency based on the described high repeatability and deep coverage from microgram-level tissues.
• Analyzing organ-enriched protein signatures based on the identification of functionally distinct proteins unique to each tissue.
• Comparing protein preservation effects based on the described shifts between paired FF and FFPE tissue analyses.
• Training models for protein identification from mass spectrometry data based on the large number of identified peptides and protein groups.

Strengths

• High repeatability with pairwise Pearson’s r > 0.96 across six experimental replicates.
• Deep proteome coverage identifying up to ∼10,000 protein groups and ∼150,000 peptides.
• Wide dynamic range spanning 6–7 orders of magnitude.
• Data supports a simplified workflow that processes tissues in ≤1.5 to 2 hours, reducing variability.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data is specific to mouse organ samples; applicability to human tissues may require validation.

Provenance

Source

figshare

Collection Method

Proteomic analysis using the timsTOF Pro mass spectrometer following the SWIFT tissue-preparation workflow.

Freshness

Last updated 2026-04-28 06:06:41; freshness should be verified.