Proteomics Platform Comparison Using Neonatal Mouse Lung Tissues

A comparison of next-generation mass spectrometry platforms (Orbitrap Astral, timsTOF Ultra) against an Orbitrap Exploris 480 using 12 neonatal mouse lung tissue samples. The analysis identified approximately 4000 common proteins, with next-generation platforms quantifying over 225,000 peptides and 13,000 proteins. The data demonstrates enhanced proteome depth and improved pathway coverage for systems biology assessment.

Use Cases

• Compare protein identification counts (~4000 common proteins) across four acquisition strategies (Exploris 480 DDA/DIA, Astral HR-DIA, timsTOF Ultra DIA-PASEF).
• Analyze quantified peptide (>225,000) and protein (13,000) depth differences between next-generation platforms and the Exploris 480 DDA baseline.
• Assess improvements in subcellular compartment annotations (from 30% to 66%) and reactome pathway coverage (from 58% to 90%) using next-generation DIA data.
• Identify phenotype-associated proteins enriched in mitochondrial, ribosomal, and extracellular components from differential expression analysis.
• Evaluate functional annotation bias in proteins uniquely detected by different platforms.

Strengths

• Direct comparison of four distinct mass spectrometry acquisition strategies on the same biological samples.
• Quantifies over 225,000 peptides and 13,000 proteins, representing significant depth increases over the baseline.
• Demonstrates concrete improvements in systems biology metrics, such as raising pathway coverage from 58% to 90%.

Limitations

• Dataset scale is small at 1.6 MB, suggesting it contains summary results rather than raw spectral data.
• Findings are specific to neonatal mouse lung tissues from a bronchopulmonary dysplasia model, limiting generalizability.
• The exact row and column structure of the provided XLSX file is unknown from the input.

Provenance

Source

figshare

Collection Method

Mass spectrometry analysis of neonatal mouse lung tissues from a bronchopulmonary dysplasia model (n=12), comparing platforms and acquisition methods.

Time Range

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Freshness

Last updated March 2026.

Geography

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