High-Multiplex Proteomics: Analytical Trade-Offs and a Practical Selection Framework for Emerging Platforms.
- 1Grupo de Investigación en Enfermedades Cardiorrenales y Metabólicas, Departamento de Medicina y Cirugía, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, 46115 Valencia, Spain.
Abstract
Classical liquid chromatography-tandem mass spectrometry (LC-MS/MS) remains a cornerstone of proteomics, but deep profiling of complex biofluids is constrained by the extreme dynamic range of protein abundance and low sample throughput. Emerging high-multiplex platforms address these limitations through distinct high-throughput configurations, including antibody-based proximity assays, modified aptamers, nanoparticle-assisted mass spectrometry, and digital single-molecule immunoassays. Despite their discovery potential, these technologies operate within alternative bottom-up or affinity-based frameworks, meaning that they are not interchangeable. Quantitative measurements of nominally identical proteins frequently show poor to moderate cross-platform agreement, reflecting fundamental differences in chemistry, epitope accessibility, matrix susceptibility, genetic variants, and peptide-level protein inference. Crucially, because these platforms generally yield aggregate quantitative readouts, they typically average across the proteoform spectrum, limiting their ability to differentiate whether an abundance shift is driven by specific splice variants, localized post-translational modifications, or a uniform increase in the protein's overall concentration. This review provides a balanced, decision-oriented comparison of the Olink Proximity Extension Assay, SomaLogic SomaScan, Seer Proteograph and Quanterix Simoa, delineating their operational utility alongside their respective technical limitations. We propose a practical framework to guide platform selection based on the specific biological question, cohort size, and required structural resolution, while evaluating strategies to enhance cross-platform reproducibility via standardized reference matrices, structure-informed interpretation, and multi-tiered validation workflows.
Related
- A predictive transferability index for crystal plasticity framework selection: Variational derivation, analytical bounds, and FFT-based plausibility assessment
- Mass Spectrometry-Based Structural Proteomics and Analytical Ultracentrifugation Characterize the Structures of Oligomeric Apolipoprotein E4 and its Variants
- Comparative assessment of Au- and Ag-based SERS substrates for cancer and disease diagnosis: A review on analytical performance, reproducibility, and practical challenges
- A transferable perturbation proteomics framework for phenotype- 1 based annotation and antiproliferative potency scoring of antineoplastic agents
- DeepHeal: An Interpretable Framework for Phenotype-Based Antineoplastic Drug Discovery Using Drug-Perturbation Proteomics
BibTeX
@article{okojie2026highmultiplex,
title = {{High-Multiplex Proteomics: Analytical Trade-Offs and a Practical Selection Framework for Emerging Platforms.}},
author = {Owahabanun-Joshua Okojie and Ana Checa-Ros and Luis D'Marco},
journal = {Proteomes},
year = {2026},
month = sep,
doi = {10.3390/proteomes14040051},
url = {https://europepmc.org/article/MED/42924749},
note = {CC BY},
}
RIS
TY - JOUR
TI - High-Multiplex Proteomics: Analytical Trade-Offs and a Practical Selection Framework for Emerging Platforms.
AU - Owahabanun-Joshua Okojie
AU - Ana Checa-Ros
AU - Luis D'Marco
PY - 2026
DA - 2026/09/29
JO - Proteomes
DO - 10.3390/proteomes14040051
UR - https://europepmc.org/article/MED/42924749
AB - Classical liquid chromatography-tandem mass spectrometry (LC-MS/MS) remains a cornerstone of proteomics, but deep profiling of complex biofluids is constrained by the extreme dynamic range of protein abundance and low sample throughput. Emerging high-multiplex platforms address these limitations through distinct high-throughput configurations, including antibody-based proximity assays, modified aptamers, nanoparticle-assisted mass spectrometry, and digital single-molecule immunoassays. Despite their discovery potential, these technologies operate within alternative bottom-up or affinity-based frameworks, meaning that they are not interchangeable. Quantitative measurements of nominally identical proteins frequently show poor to moderate cross-platform agreement, reflecting fundamental differences in chemistry, epitope accessibility, matrix susceptibility, genetic variants, and peptide-level protein inference. Crucially, because these platforms generally yield aggregate quantitative readouts, they typically average across the proteoform spectrum, limiting their ability to differentiate whether an abundance shift is driven by specific splice variants, localized post-translational modifications, or a uniform increase in the protein's overall concentration. This review provides a balanced, decision-oriented comparison of the Olink Proximity Extension Assay, SomaLogic SomaScan, Seer Proteograph and Quanterix Simoa, delineating their operational utility alongside their respective technical limitations. We propose a practical framework to guide platform selection based on the specific biological question, cohort size, and required structural resolution, while evaluating strategies to enhance cross-platform reproducibility via standardized reference matrices, structure-informed interpretation, and multi-tiered validation workflows.
SN - 2227-7382
ER -