Proteomics Platform Comparison Using Neonatal Mouse Lung Tissue

A study comparing next-generation mass spectrometry platforms for proteomics analysis. The research quantified over 225,000 peptides and 13,000 proteins from 12 neonatal mouse lung tissue samples, demonstrating enhanced proteome depth. The analysis employed four acquisition strategies across three instrument platforms.

Use Cases

• Compare peptide and protein quantification depth across platforms like Orbitrap Astral and timsTOF Ultra using the reported >225,000 peptides and 13,000 proteins metrics.
• Analyze the impact of acquisition strategies (DDA/DIA, HR-DIA, DIA-PASEF) on proteome coverage, referencing the 98% coverage and 92% concordance findings.
• Assess improvements in subcellular compartment annotation and Reactome pathway coverage, using the reported increase from 30% to 66% and 58% to 90%.
• Identify phenotype-associated proteins and enriched pathways from differential expression analysis, referencing the up to 44 enriched pathways finding.

Strengths

• Quantified over 225,000 peptides and 13,000 proteins, representing significant analytical depth.
• Demonstrated 98% proteome coverage of DDA identifications using DIA methods and 92% concordance between next-generation systems.
• Enhanced subcellular compartment annotations from 30% to 66% and Reactome pathway coverage from 58% to 90%.

Limitations

• Dataset is small in scale at 5.5 MB, limiting the volume of raw spectral data available.
• Analysis is specific to neonatal mouse lung tissue from a bronchopulmonary dysplasia model, limiting generalizability.
• The exact row and column structure of the underlying data tables is unknown.

Provenance

Source

Filipa Blasco Tavares Pereira Lopes via figshare

Collection Method

Mass spectrometry analysis of neonatal mouse lung tissues using multiple platforms and acquisition strategies.

Time Range

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Freshness

Last updated March 2026.

Geography

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