Comparison of Proteomic Assessment Methods in Multiple Cohort Studies

Area of Science:

• Biochemistry
• Proteomics
• Biotechnology

Background:

• Novel aptamer-based proteomics platforms, such as SOMAscan, are increasingly popular for high-throughput protein quantification.
• Comparisons between these novel platforms and conventional immunoassays are limited, creating uncertainty for cross-assay data interpretation.

Purpose of the Study:

• To explore the correlation between results from multiplex immunoassays and the SOMAscan proteomics platform.
• To assess the appropriateness of cross-assay comparisons in proteomics research.

Main Methods:

• Spearman correlation coefficients were calculated for 63 proteins across two chronic obstructive pulmonary disease (COPD) cohorts (SPIROMICS and COPDGene) using multiplex immunoassays and SOMAscan.
• Additional comparisons were made using immunoassays in the Multi-Ethnic Study of Atherosclerosis and between Olink and SOMAscan platforms in myocardial infarction patients.
• cis pQTL data, mass spectrometry, and public data were integrated to analyze correlation patterns.

Main Results:

• Spearman correlation coefficients between SOMAscan and immunoassays ranged widely from -0.13 to 0.97, with a median of approximately 0.5.
• Consistent correlation patterns were observed across different cohorts and assay types.
• Comparisons between the Olink and SOMAscan platforms also revealed a broad range of correlations.

Conclusions:

• The correlation between different proteomics assays, including aptamer-based and antibody-based platforms, varies significantly.
• Researchers must carefully consider assay-specific correlations when comparing or meta-analyzing proteomics data from multiple studies or platforms.