A mouse plasma peptide atlas as a resource for disease proteomics

Area of Science:

• Proteomics
• Biochemistry
• Genomics

Background:

• Plasma proteome analysis is crucial for understanding biological functions and disease.
• Existing mouse plasma proteomic data is limited, hindering comprehensive research.

Purpose of the Study:

• To create a comprehensive, publicly accessible repository of mouse plasma proteomic data.
• To identify novel peptides, proteins, isoforms, and transcript variants in mouse plasma.
• To establish a high-confidence dataset for future research and biomarker discovery.

Main Methods:

• Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed for high-throughput proteomic analysis.
• Extensive data processing and high-confidence peptide/protein identification were performed.
• A repository of 568 LC-MS/MS runs was established, containing data for 13,779 distinct peptides and ~3,000 proteins.

Main Results:

• Identification of 13,779 high-confidence distinct peptides and approximately 3,000 proteins.
• Quantification revealed a 7-logarithmic range of protein abundance in mouse plasma.
• Discovery of novel protein isoforms and transcript variants not predicted by prior genome analysis.

Conclusions:

• The developed mouse plasma proteomic repository significantly enhances available research resources.
• The identified novel isoforms and variants offer new avenues for investigating gene regulation and function.
• This work provides a foundation for future studies in mouse physiology, disease, and drug development.