Abstract
The plasma proteome is the ultimate target for biomarker discovery. It stores an endless amount of information on the pathophysiological status of a living organism, which is however still difficult to comprehensively access. The high structural complexity of the plasma proteome can be addressed by either a system-wide and unbiased tool such as mass spectrometry (LC-MS/MS) or a highly sensitive targeted immunoassay such as the Proximity Extension Assays (PEA). In order to address relevant differences and important shared characteristics, we tested the performance of LC-MS/MS in data-dependent and -independent acquisition modes and PEA Olink to measure circulating plasma proteins in 173 human plasma samples from a Southern German population-based cohort. We demonstrated the measurement of more than 300 proteins with both LC-MS/MS approaches applied, mainly including high abundance plasma proteins. By the use of the PEA technology, we measured 728 plasma proteins, covering a broad dynamic range with high sensitivity down to pg/ml concentrations. In a next step, we quantified 35 overlapping proteins with all three analytical platforms, verifying the reproducibility of data distributions, measurement correlation and gender-based differential expression. Our work highlights the limitations and the advantages of both, targeted and untargeted approaches, and prove their complementary strengths. We demonstrated a significant gain in proteome coverage depth and subsequent biological insight by platforms combination – a promising approach for future biomarker and mechanistic studies.
Abbreviation
- PEA
- Proximity Extension Assay
- DDA
- Data-dependent acquisition
- DIA
- Data-independent acquisition
- LC-MS/MS
- liquid chromatography mass spectrometry
- FDR
- false discovery rate
- ID
- identification
- KORA
- Cooperative Health Research in the Region of Augsburg
- Olink panels
- C-MET cardiometabolic; CVDII cardiovascular II; CVDIII cardiovascular III; ONCII oncology II; ONCIII oncology III; DEV development; IMM immune response; NEU neurology