Rethinking Clinical Protein Assays: ELISA vs. Mass Spectrometry

The field of protein detection and measure is rapidly evolving, enabled by advances in instrumentation, methodological improvements, and greater computational capacities. The scope of clinical protein assays (ELISA, etc.), in particular, has expanded in many therapeutic areas with the use of protein biomarkers in pharmacodynamic studies, as companion diagnostics, and to predict and monitor treatment response in clinical trials.

Achieving the assay sensitivity needed for clinical studies has traditionally been challenging in proteomics, due in part to the wide dynamic range of proteins in biological samples. Moreover, with greater interest in specific protein isoforms, or proteoforms, there is increasing need for greater specificity in measure, in particular being able to discriminate variants from ‘wild-type’ proteins. Technical hurdles across methods limit the ability to effectively address all these demands, often leading to trade-offs between sensitivity, specificity, and throughput. 

For example, ELISA has been long-considered the gold standard to quantify clinically-relevant proteins due to its high sensitivity, but the antibody pairs used to amplify the signal of low-concentration analytes can have issues with cross-reactivity and non-specific binding, limiting specificity. Traditional mass spectrometry, on the other hand, offers excellent specificity through its ability to fragment proteins for peptide-level sequencing, but has historically been a slow method that lacked the sensitivity to capture low-abundance proteins.

In this paper, we discuss the advancements that have occurred in mass spectrometry-based proteomics within the last two years that are mitigating analytical trade-offs by delivering the depth, sensitivity, and reproducibility required for clinical protein assays.