Mouse Lung Proteomics Comparison of Next-Generation Mass Spectrometry Platforms

A proteomics study compares next-generation mass spectrometry platforms (Orbitrap Astral, timsTOF Ultra) against an Orbitrap Exploris 480 using neonatal mouse lung tissues from a bronchopulmonary dysplasia model (n=12). The analysis employed four acquisition strategies, identifying ~4000 common proteins and quantifying over 225,000 peptides and 13,000 proteins on the new platforms.

Use Cases

• Compare protein quantification depth across platforms like Orbitrap Astral and timsTOF Ultra, which quantified >225,000 peptides.
• Analyze proteome coverage improvements, where next-generation platforms increased subcellular compartment annotations from 30% to 66%.
• Perform differential expression analysis to identify phenotype-associated proteins, enriched in mitochondrial and ribosomal components.
• Assess Reactome pathway coverage, which improved from 58% with DDA to 90% with next-generation DIA platforms.
• Evaluate acquisition strategy performance (e.g., DDA, DIA, DIA-PASEF) on common protein identifications (~4000 proteins).

Strengths

• Benchmark data from 12 biological replicates (neonatal mouse lung tissues).
• Quantifies over 225,000 peptides and 13,000 proteins on next-generation platforms.
• Demonstrates a 92% concordance rate between the two next-generation systems.
• Shows substantial improvements in systems biology metrics like pathway coverage.

Limitations

• Limited to a single tissue type (neonatal mouse lung) and one disease model, reducing generalizability.
• Sample size of 12 biological replicates, while sufficient for the study, is modest for broad statistical inference.
• Data is contained in a 6.9 MB XLSX file, indicating a processed summary rather than raw spectral data.

Provenance

Source

figshare, authored by Filipa Blasco Tavares Pereira Lopes.

Collection Method

Experimental comparison using four mass spectrometry acquisition strategies on mouse lung tissue.

Time Range

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Freshness

Last updated March 2026.

Geography

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