Proteomics Platform Comparison Using Neonatal Mouse Lung Tissues

A study comparing next-generation mass spectrometry platforms (Orbitrap Astral, timsTOF Ultra) against an Orbitrap Exploris 480 for proteomic analysis of neonatal mouse lung tissues from a bronchopulmonary dysplasia model (n=12). The platforms identified approximately 4000 proteins in common, with Orbitrap Astral and timsTOF Ultra quantifying over 225,000 peptides and 13,000 proteins.

Use Cases

• Compare protein quantification depth across platforms using the quantified >225,000 peptides and 13,000 proteins metrics.
• Analyze platform-specific proteome coverage improvements, from 30% to 66% for subcellular compartment annotations.
• Assess differential expression results for phenotype-associated proteins enriched in mitochondrial, ribosomal, and extracellular components.
• Evaluate pathway coverage enhancements in DIA data sets, from 58% to 90% for reactome pathway coverage.
• Investigate the absence of functional annotation bias in proteins uniquely detected by each platform.

Strengths

• Direct comparison of four specific acquisition strategies: Exploris 480 DDA/DIA, Astral HR-DIA, and timsTOF Ultra DIA-PASEF.
• Quantifies over 225,000 peptides and 13,000 proteins using next-generation platforms.
• Demonstrates substantial improvements, such as increasing subcellular compartment annotations from 30% to 66%.
• Shows high concordance (92%) between next-generation systems and 98% proteome coverage of DDA identifications using DIA methods.

Limitations

• Dataset is small in file size (339.4 KB), indicating limited raw data or aggregated results rather than extensive primary data.
• Analysis is restricted to a single biological model (neonatal mouse lung from bronchopulmonary dysplasia, n=12), limiting generalizability.
• Specific row and column counts for the underlying data tables are unknown.

Provenance

Source

Filipa Blasco Tavares Pereira Lopes via figshare.

Collection Method

Experimental comparison using neonatal mouse lung tissues from a disease model, analyzed with multiple mass spectrometry platforms and acquisition strategies.

Time Range

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Freshness

Last updated March 26, 2026.

Geography

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