A Carrier-Based Quantitative Proteomics Method Applied to Biomarker Discovery in Pericardial Fluid

Area of Science:

• Proteomics
• Biochemistry
• Cardiovascular Research

Background:

• Liquid chromatography tandem mass spectrometry faces challenges in quantifying diverse protein concentrations in biofluids.
• Pericardial fluid presents a complex matrix for comprehensive proteomic analysis.

Purpose of the Study:

• To adapt the SCoPE (Single-Cell Proteomics) method using a myocardial tissue carrier for improved protein quantification in pericardial fluid.
• To investigate protein expression profiles in pericardial fluid from patients with type 2 diabetes mellitus and/or heart failure.

Main Methods:

• Adaptation of the SCoPE method with a myocardial tissue carrier for pericardial fluid analysis.
• Isobaric labeling of carrier proteome and patient samples for distinct quantification.
• Comparison of traditional liquid chromatography tandem mass spectrometry with the carrier proteome approach.

Main Results:

• Quantification of 1398 proteins with the carrier method versus 265 without, with a higher proportion of myocardial proteins identified.
• A nearly four-fold increase in the number of differentially expressed proteins detected.
• Pathway analysis revealed enrichment of immune activation, blood coagulation, and stress pathways in patients with co-existing heart failure and type 2 diabetes mellitus.

Conclusions:

• The carrier proteome approach significantly enhances protein quantification in challenging biological matrices like pericardial fluid.
• This method holds potential for advancing biomarker discovery in cardiovascular diseases.
• Mass spectrometry data are publicly available via ProteomeXchange (PXD053450).