SWIFT Workflow: Proteomic Data from Microgram-Level FF and FFPE Mouse Tissues

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, results from a fast, simplified tissue preparation workflow called SWIFT. It includes data from both fresh-frozen and formalin-fixed, paraffin-embedded tissues, with high repeatability reported (pairwise Pearson's r > 0.96).

Use Cases

• Benchmarking proteomic sample preparation workflows based on reported protein group and peptide counts.
• Analyzing organ-enriched protein signatures based on the identification of functionally distinct proteins unique to each tissue.
• Studying preservation-induced shifts in protein detection by comparing paired FF and FFPE tissue data.
• Evaluating method repeatability based on the reported high pairwise correlation across experimental replicates.

Strengths

• High proteome depth, identifying up to ~10,000 protein groups and ~150,000 peptides.
• Demonstrated high repeatability with pairwise Pearson's correlation > 0.96 across six experimental replicates.
• Covers two critical tissue preservation types: fresh-frozen (FF) and formalin-fixed, paraffin-embedded (FFPE).

Limitations

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

Provenance

Source

figshare, author Chuping Wei.

Collection Method

Data generated via the SWIFT (Simple Workflow for Integrated and Fast Tissue-preparation) protocol and analyzed on a timsTOF Pro mass spectrometer.

Freshness

Last updated 2026-04-28 06:06:46; freshness should be verified.