Proteins mediate signaling, serve as drug targets, and drive phenotypic outcomes, making their accurate measurement a critical part of drug development.
With our mass spectrometry-based proteomics services, Sapient provides direct, quantitative measures of proteins and their proteoforms with unmatched depth, scale, and specificity for robust, reproducible results.
Our workflows detect thousands of proteins in a wide range of sample matrices, capturing the molecular signatures that traditional platforms often miss – enabling clearer insights into pathways, mechanisms, and disease biology.
Despite the importance of accurate protein quantification in validating protein targets and biomarkers, many studies still rely on indirect approaches to profile the proteome.
RNA is often used as a surrogate measure for protein abundance, but there is clear evidence that mRNA and protein levels often poorly correlate, particularly in disease or treatment-altered states. This disconnect means that relying on transcriptomics alone can lead teams to prioritize biomarkers and targets that fail to translate.
Antibody-based approaches like immunohistochemistry (IHC) or affinity proteomics are indirect in that they measure an antibody’s interaction with the target protein rather than the protein itself. While valuable in many contexts, these methods can be limited by non‑specific binding and cross‑reactivity, and are often blind to protein isoforms or PTMs that may be critical to disease biology or therapeutic response.
Sapient leverages next-generation mass spectrometry to fill these gaps.
Direct protein profiling using advanced mass spectrometry – including proteoforms/PTMs
Exceptional depth and dynamic range to robustly measure thousands of proteins per sample
Applicability in diverse sample matrices
High‑throughput workflows for rapid scalability
Integrated support from discovery through validation
Contextualization of findings in DynamiQ™
The result? De-risked translation with accurate, actionable views of functional biology.
Explore the innovation cycles that have converged to close the gap between what mass spectrometry could theoretically deliver as a discovery proteomics platform, and what it now routinely achieves at scale – and its practical advantages for drug development compared to antibody- and aptamer-based approaches.
Providing ultra‑deep proteome coverage across matrices to capture differentially expressed proteins, PTMs, and isoforms.
We leverage labeled peptides for direct, absolute quantitation of proteins of interest, including for multiplexed panels.
Sapient can further accelerate translation of identified targets and biomarkers with cross-validation in a real-world cohort.
See what our combination of next-generation mass spectrometry & large-scale human biology data can deliver.
Sapient directly measures proteins and their proteoforms using advanced mass spectrometry rather than relying on RNA as a proxy or on affinity‑based assays that use antibodies for indirect protein measure. This approach delivers more accurate and reproducible protein quantification, with the ability to resolve isoforms and PTMs that other platforms often miss.
When comparing our method to traditional mass spectrometry, Sapient has made significant technological advancements across sample handling, protein extraction, mass spectrometry hardware, and software to improve throughput and sensitivity, even in sample matrices with broad dynamic range. Our workflows are proven to deliver high-precision, tightly QC’ed proteomics datasets at scale.
Mass spectrometry-based proteomics is moving from a bespoke research tool into a core pillar of biopharma drug development, driven by improvements in instrument sensitivity, throughput, and data analysis. While mass spectrometry has always had critical advantages for protein measurement – no antibody
requirement, direct sequence confirmation, no panel limitations – they can now be realized at scale.
The practical consequence for biopharma is that discovery proteomics is becoming the default first look at the proteome across target identification, biomarker discovery, mechanism-of-action studies, and translational programs. Unlike affinity-based panels, mass spectrometry captures post-translational modifications, distinguishes proteoforms and isoforms, and accesses the dark proteome — regions that lack validated antibodies but are increasingly implicated in disease biology.
As the platform has matured, the most significant shift is in its integration into clinical-stage programs: biomarker panels discovered via mass spectrometry can transition directly into targeted MS assays for validation, creating an end-to-end proteomics workflow that preserves biological relevance from early discovery through the clinic. This is critical to the future of mass spectrometry-based proteomics in biopharma – providing a value proposition both distinct from and complementary to genomics, RNA sequencing, and affinity-based proteomics platforms.
RNA ≠ protein. Studies have continually shown that mRNA and protein levels are often poorly correlated, because protein abundance and activity often shift independently of RNA due to post‑transcriptional regulation, alternative splicing, protein degradation, and post‑translational modifications. While RNA can predict potential protein activity, direct protein profiling reveals the true functional state of a cell or tissue.
Immunohistochemistry (IHC) is deeply embedded in clinical workflows and affinity‑based methods have proven quite powerful for discovery of new protein biomarkers and targets. These approaches, however, measure an antibody’s interaction with a target protein rather than the protein itself, which can introduce challenges such as non‑specific binding and antibody cross-reactivity. It can also be costly and time-consuming to develop antibodies that can detect protein isoforms or PTMs.
Sapient’s mass spectrometry-based workflows overcome these constraints to provide complementary data that expands upon IHC and affinity-based analyses by significantly improving quantitative fidelity while offering a means to readily measure PTMs or protein variants that may underlie disease heterogeneity or treatment response and resistance.
Our proteomics workflows can be applied across a wide range of matrices including plasma/serum, tissues, tumors, FFPE samples, CSF, saliva, urine, and cells/media. This flexibility enables broad discovery and targeted measurement across preclinical, translational, and clinical studies.
DynamiQ provides a population-scale molecular‑clinical database in which to confirm findings uncovered in your study.
Identified proteins of interest can be cross‑validated in independent human cohorts, enabling rapid confirmation of disease relevance, clinical associations, and translational potential. This significantly de‑risks target and biomarker advancement.
In addition to our pre-characterized samples, Sapient’s DynamiQ Tumor-Tissue virtual biobank offers streamlined access to clinically annotated FFPE tumors and tissues across common and rare diseases. Reach out if you are interested in leveraging these analysis-ready samples, reach out to our team.
Absolutely. As a multi‑omics partner, Sapient can integrate our proteomics services with metabolomics, lipidomics, cytokine profiling, and DNA/RNA sequencing to build comprehensive mechanistic insight from regulation through downstream functional outcomes.
Connect with our scientists to discuss your project or the biological questions you want to answer. We’re here to help you design and execute a high-impact study.
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