Proteomics Platform Comparison Using Neonatal Mouse Lung Tissues

A study by Filipa Blasco Tavares Pereira Lopes compares next-generation mass spectrometry platforms (Orbitrap Astral, timsTOF Ultra) against an Orbitrap Exploris 480. The analysis, using neonatal mouse lung tissues from a bronchopulmonary dysplasia model (n=12), found the new platforms quantified over 225,000 peptides and 13,000 proteins, representing 800% and 300% greater depth than the older system.

Use Cases

• Compare protein quantification depth across platforms 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 and subcellular compartment annotation rates.
• Assess differential expression results for phenotype-associated proteins enriched in mitochondrial, ribosomal, and extracellular components.
• Evaluate platform concordance using the reported 92% agreement between next-generation systems and 98% DIA coverage of DDA identifications.

Strengths

• Direct comparison of four distinct acquisition strategies across three major mass spectrometry platforms.
• Quantified over 225,000 peptides and 13,000 proteins, representing up to 800% greater depth than the reference platform.
• Demonstrated improved systems biology assessment, raising subcellular compartment annotations from 30% to 66% and reactome pathway coverage from 58% to 90%.

Limitations

• Limited biological scope, focused solely on neonatal mouse lung tissues from a single disease model (n=12).
• Small data file size (12.0 KB) indicates the dataset contains summary results, not the underlying raw spectral data.

Provenance

Source

Filipa Blasco Tavares Pereira Lopes via figshare

Collection Method

Experimental comparison using neonatal mouse lung tissues from a bronchopulmonary dysplasia model, employing four different mass spectrometry acquisition strategies.

Time Range

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Freshness

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Geography

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