Proteomics Biomarkers Beyond Blood

By Jan Schejbal, senior scientist, AbbVie

Biomarkers have been a cornerstone of drug discovery research that is often outshined by the promise of novel targets. Despite this, it's often the robustness and reliability of biomarkers that determine the pace and success of both preclinical and clinical projects. Effective biomarker strategies have the potential to accelerate decision-making, de-risk development, and help drive precision medicine.

While biomarker selection, assay optimization, and data interpretation are all essential and complex topics that each deserve dedicated discussion, this article will focus on an often underappreciated aspect: the choice of biological matrix for biomarker discovery and quantification. Herein, I will highlight how recent advances in mass spectrometry (MS)-based proteomics are enabling us to move beyond traditional blood samples, opening new avenues for more patient-centric, informative, and actionable biomarker research.

Why Blood? The Ubiquity And Limitations Of The Default Matrix

Blood is the most commonly used matrix for biomarker studies — and with good reasons:

• Blood collection is a familiar, minimally invasive, and clinically accepted practice. Most patients anticipate blood draws as part of healthcare, making the biofluid highly accessible.
• Decades of routine use have generated tremendous historical data sets, empowering researchers to understand baseline variability, clinical thresholds, and pathophysiological trends.
• Analytical workflows for blood-derived matrices (e.g., plasma, serum, and blood cells) are well standardized, paving the way for study comparability, logistical efficiency, and regulatory acceptance.

However, blood's universality masks some key limitations. The circulatory system essentially acts as a collection highway, picking up diverse biomolecules as blood moves through the body. This can dilute organ- or tissue-specific signals, sparking major challenges in biomarker specificity and sensitivity. To use an analogy: shopping in a vast bazaar and buying mixed fruit from many stalls makes it difficult to trace the origin, or quality, of a single item in your basket. Similarly, blood can carry markers from numerous sources, often making it difficult to localize the exact origin of a critical molecule. Biomarkers present at low concentrations in the circulation may be highly enriched at their tissue of origin, leading to missed opportunities if blood remains the sole focus.

Many disease processes are fundamentally local, involving highly specific tissue microenvironments or intercellular signaling networks, such as the extracellular matrix (ECM). Relying exclusively on blood can mean missing the richness and nuance of localized biological events. This realization is fueling interest in alternative matrices that can capture more proximal context-relevant information, especially for diseases where blood signals are diluted or nonspecific.

Moving Beyond Blood: Creative Approaches And The Need For Innovation

Traditionally, the search for localized biomarkers outside of blood has focused on tissue biopsies. While biopsies offer direct access to the site of disease, they are often invasive, difficult to perform routinely, and can pose ethical or feasibility concerns — particularly outside fields like oncology where tissue removal may be justified and is often beneficial. For many therapeutic areas, frequent or large-scale tissue acquisition is simply not an option. This reality compels teams to seek creative, minimally invasive, and patient-centric strategies to access relevant biology without undue burden.

Harnessing The Power Of Mass Spectrometry (MS)-Based Proteomics

A major driver of innovation in biomarker discovery has been the unprecedented progress in MS-based proteomics. Over the last five years, technological advancements have radically enhanced throughput, sensitivity, and data reliability. Where studies were once restricted to small cohorts and could only detect a few hundred proteins, it is now possible to interrogate deep proteomes from hundreds or even thousands of patient samples in a single study, even in difficult matrices. This has opened the door to studying new biofluids and tissues, making routine proteome profiling a realistic prospect for clinical research teams.

One of the main differentiators of MS proteomics compared to affinity-based panels (e.g., proximity extension assays or aptamer panels) is its unbiased detection of proteins and post-translational modifications. MS does not depend on preexisting antibodies or affinity reagents. It can identify novel peptides, isoforms, and modifications, directly expanding our understanding of biological mechanisms and candidate biomarkers. Moreover, complementing affinity assays with MS provides deeper validation and can mitigate false positives or negatives due to off-target recognition or limited panel coverage.

Case Study 1: Tears — A Window Into Ophthalmology And Neurology

Tears offer a powerful, yet underutilized, matrix for biomarker research. In ophthalmology, they are especially attractive because collection (using Schirmer’s strips, for example) is fast, minimally invasive, and causes little patient discomfort. Furthermore, tears are much more specific to local disease biology in the eye compared to blood while being just as easily accessible for repeated sampling.

When my team first began analyzing tear samples several years ago, technical and logistical limitations kept us to small cohorts, detecting only around 500 proteins per sample in less than a dozen samples. Still, we were able to identify most biomarkers previously reported in the literature for our target indication. However, in a more recent pilot leveraging modern MS technology, we processed 35 tear samples and quantified a median of about 4,000 proteins in each. To our surprise, all previously reported biomarkers clustered among the most highly abundant proteins, with over half in the top 1% by signal intensity. This prompts an important caution for project teams: initial findings often reflect technological limitations or detection bias, not necessarily genuine biological difference. Teams should consider protein abundance when defining candidate biomarkers, especially in novel or data-poor matrices.

This broader, deeper coverage provided additional benefits: for the first time, we detected proteins involved in key signaling cascades, enabling us to propose direct target engagement biomarkers now under further evaluation. Additionally, we were intrigued to find numerous proteins linked with central nervous system processes, hinting at the potential for tears to serve as an accessible matrix even in neurological drug development. Our experience with tears demonstrates how new matrices, when paired with advanced MS proteomics, can yield surprisingly rich, actionable data.

Case Study 2: Skin Tape Strips — Revolutionizing Dermatology Biomarkers

In dermatology, the search for robust biomarkers faces a unique set of challenges. Blood-based markers are often too diluted to reflect skin-specific pathophysiology, while biopsies, even though technically accessible, are far from ideal: they are invasive, heal slowly in diseased skin, and lead to sample attrition due to frequent patient consent withdrawals. This makes collection of sufficient and consistent sample cohorts daunting, often limiting study power and interpretability.

Skin tape strips offer an elegant alternative, allowing for the superficial sampling of affected skin with only minor, fleeting discomfort and minimal risk. Despite historical obstacles — primarily low and variable amounts of sampled proteins — advances in MS sensitivity now allow for robust proteomic quantification. Our team’s work on tape strips started by an encounter with a problematic data set from external collaborations exhibiting high variability and poor proteome coverage. We decided to develop an internal workflow and through diligent optimization of sample processing we are now able to reliably detect up to 1,500 proteins in even the most challenging samples. Healthy skin revealed ~1,700 proteins per strip, and interestingly, the proteome was remarkably stable across up to 10 consecutive strips. Contrary to initial expectations that early strips would differ due to sampling superficial cells, we found that only a few tapes are sufficient to comprehensively capture the skin proteome. This has meaningful implications for study design and patient compliance: only a couple of strips are needed for high-quality data, reducing participant burden and potentially enhancing cohort retention.

Ultimately, demonstrating clinical relevance and linking biomarker changes in novel matrices to meaningful patient outcomes remains a key challenge and an important next step for translational success. Our ongoing projects are thus further exploring the utility of tape strips for biomarker discovery in a variety of dermatological conditions. We believe their accessibility, minimal invasiveness, and compatibility with MS proteomics position them as a transformative tool for precision dermatology.

Practical Considerations And Actionable Recommendations

• Matrix selection is critical: Teams should move beyond convenience and consider which fluids or tissues are most relevant to disease biology while also keeping patient comfort and compliance in mind.
• Collaborate closely with analytical and bioinformatics experts when working in novel matrices. Optimizing sample collection, standardization, and data interpretation is vital for robust results.
• Interpret literature, especially studies based on small cohorts or previous generation technologies, with a critical eye. Detection limits, sample handling, and analytical bias can all influence reported findings.
• Use MS proteomics synergistically with affinity-based methods. Together, they offer broader discovery, deeper validation, and crucial orthogonal corroboration.
• Don’t underestimate the value of pilot studies to tailor protocols for your unique matrix or disease area.
• Teams should recognize that regulatory qualification and clinical adoption of novel matrix biomarkers may require tailored validation strategies distinct from those used for blood-based markers.

Looking Forward: The Future Of Biomarker Discovery Is Patient Centric

The push toward less invasive, more biologically relevant sampling, enabled by the growing power and accessibility of MS proteomics, is set to redefine biomarker research over the coming decade. By pairing novel matrices with unbiased, highly sensitive technologies, we can generate richer data sets, drive innovation in clinical study designs, and ultimately deliver more personalized and effective therapies. Beyond tears and skin tape strips, emerging matrices such as saliva, urine, and exhaled breath condensate offer additional avenues for biomarker discovery and may benefit from similar approaches. As researchers, our mission is to keep patient well-being at the center of our efforts, balancing scientific discovery with empathy and practicality. Every technological leap, every new pilot, brings us a step closer to earlier diagnoses, more predictive drug development, and a reduced burden for the patients.

Acknowledgement

Many of these thoughts we conceived and refined during thoughtful conversations and mentoring sessions with Matt Blatnik. I sincerely appreciate Matt’s insight and expertise.

About The Author

Jan Schejbal, Ph.D., is a senior scientist at AbbVie, leading mass spectrometry-based proteomics within the Developmental Sciences organization. He earned his Ph.D. in biochemistry in 2018 from Masaryk University in Brno, Czech Republic, and continued as a postdoctoral fellow in Alexander Ivanov’s lab at the Barnett Institute in Boston, focusing on proteomics of limited samples. Since joining AbbVie in 2020, Jan advanced from bench scientist to center-of-excellence leader, spearheading proteomics applications in the preclinical phase of drug development across diverse therapeutic areas. He is passionate about advancing proteomics technology and fostering collaborative innovation in drug discovery.