Plasma biomarker discovery sits at the heart of precision medicine, drug development, and translational research. Yet despite decades of innovation, discovering robust, clinically actionable plasma biomarkers remains one of the most difficult challenges in proteomics.
Why? Because plasma is both the most clinically relevant biofluid and the most analytically complex.
In this blog article, we explore how combining two complementary technologies — affinity-based platforms such as NULISA™, Olink®, and SomaLogic®, and unbiased mass spectrometry (MS) — can unlock deeper insights into the plasma proteome, ultimately enabling more robust and informative biomarker discovery.
Why Plasma Proteins Matter Most for Biomarker Discovery
Proteins are highly informative plasma biomarkers. They drive biological processes, mediate disease mechanisms, and are often therapeutically actionable. Protein-level changes provide the clearest link between molecular biology and clinical outcomes.
Plasma is also clinically accessible: samples are inexpensive, minimally invasive, and well tolerated. Longitudinal sampling is feasible, enabling richer datasets for biomarker discovery, target identification, and systems-level insights into disease progression and treatment response.
The Challenge of Plasma Proteomics
Plasma proteins span over 10 orders of magnitude in concentration. A few highly abundant proteins mask thousands of low-abundance species, many of which carry the most disease-relevant information. Detecting and quantifying these rare proteins is technically demanding.
Success requires technologies that are sensitive, reproducible, and high-throughput, capable of both uncovering novel proteins and accurately measuring the most critical biomarkers.
Two leading technologies have come to the forefront to tackle these challenges: affinity-based platforms and mass spectrometry (MS)-based methods.
Affinity-Based Platforms: Targeted and High-Throughput
Affinity-based technologies such as NULISA (Biognosys certified provider), SomaScan (SomaLogic), and Olink Explore use antibodies or aptamers to detect predefined sets of proteins.
Main advantages:
- High-throughput measurements
- Small sample volume requirements
- Multiplexed analysis of thousands of proteins
- Targets well-characterized proteins in predefined panels
However, affinity-based assays are inherently targeted and hypothesis-driven, meaning discovery is limited to proteins for which high-quality binding reagents exist. Assay specificity can vary depending on epitope uniqueness, probe affinity, and sample matrix effects.
Mass Spectrometry: Unbiased and Mechanistically Informative
MS measures proteins via their peptides, enabling mechanistic insight and unbiased discovery.
What makes it powerful:
- Unbiased protein identification
- Detection of proteoforms such as protein isoforms and post-translational modifications (PTMs)
- High specificity and confidence through multi-peptide confirmation
- Independence from affinity reagents, with performance continuously improved by advances in instrumentation and analytical methods
While plasma proteomics is widely used in biomarker discovery, MS becomes especially important for cerebrospinal fluid (CSF), which is in direct contact with the central nervous system and provides more disease-relevant biological information. CSF proteomics is still less well characterized than plasma, and many relevant proteins are not included in affinity-based assays due to limited panel coverage and reagent availability, restricting true biomarker discovery.
Unbiased MS overcomes these limitations through hypothesis-free CSF proteomics, facilitating the discovery of novel biomarkers, protein isoforms, and disease-specific post-translational modifications, particularly in neurological diseases and oncology.
No Single Winner: Complementary Approaches Work Best
Every method has trade-offs between depth, bias, discovery potential, scalability, and reproducibility. There’s no single “best” technology.
The most effective strategy? Combine them:
- Affinity platforms → high-throughput, targeted measurement through predefined panels
- MS → unbiased, discovery-driven analysis
This combination maximizes coverage, insight, and translational impact.
Practical Strategies
1. Start Targeted, Then Extend with Unbiased MS
One approach is to begin with affinity-based platforms to screen large cohorts and validate known pathways, followed by unbiased MS to expand discovery. MS enables identification of novel pathway members, isoforms, post-translational modifications, and unexpected proteins that fall outside predefined panels.
Affinity platforms confirm what you expect — mass spectrometry opens new horizons.
2. Start Unbiased, Then Validate
In early discovery and complex biomarker programs, starting with MS-based proteomics offers distinct advantages. While affinity platforms provide high coverage of predefined proteins and strong quantification for low-abundance targets, they are inherently limited to known panels. Untargeted MS, on the other hand, can capture proteins that fall outside predefined assays, ideal for exploring novel biology and generating hypotheses for reverse translation applications, such as uncovering resistance mechanisms or predictive biomarkers in clinical samples.
Advances in instrumentation, reproducible LC-MS workflows, and plasma enrichment technologies further facilitate deep, scalable, and reproducible profiling, making it particularly suited for early discovery programs and complex disease research. By structuring discovery first and validation second, researchers can efficiently capture both expected and unexpected biology, naturally expanding the breadth of insights from a single study.
Benchmarking Insights
A recent study in Communications Chemistry benchmarked eight proteomic technologies covering 13,000+ proteins in a healthy cohort, highlighting the complementary strengths of each platform:
- Affinity assays excel at detecting known proteins, deliver strong technical precision (low CVs), and capture nearly complete healthy plasma proteomes.
- MS-based platforms uncover low-abundance proteins beyond predefined panels, including novel isoforms and PTMs. Standardized sample prep reduces variability, ensuring reliable and reproducible results.
- Cross-platform comparisons reveal strong agreement for biologically significant proteins, including age-associated markers, UK Biobank aging clock proteins, and validated centenarian markers.
Key takeaway: No single platform captures the entire plasma proteome. Combining technologies provides a more complete and biologically informative view, maximizing discovery potential.
Enhancing MS-Based Discovery with P2 Technology
P2 enrichment technology tackles the challenges of depth, low-abundance detection, and reproducibility. By enriching proteins prior to MS analysis, P2 enables unbiased discovery without panel-driven bias.
Key advantages:
- Exceptional depth: Detects ~6,000 proteins with >90% completeness, including low-abundance biomarkers
- High precision: Reliable quantification and strong linearity in benchmarking
- Scalable workflows: Processes up to 192 plasma samples/day with automation-ready platforms
- Robust & reproducible: Consistent results across plates and days
- Flexible access: Available as a ready-to-use kit or via CRO services
Impact: P2 enables deep, reproducible, and scalable MS-based discovery, uncovering low-abundance proteins and novel biology. For example, combining P2 with Olink Explore detected over 7,000 proteins in an oncology study, providing a more comprehensive and detailed view of the plasma proteome — ideal for biomarker discovery, pathway analysis, and translational research.
