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bioRxiv · 10.64898/2026.09.10.750723

Atlas of Proteomic Technologies: an evidence-based framework for selecting and combining commercial proteomics platforms

Whelan, C. D.·Smith-Byrne, K.
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Abstract

High-throughput proteomics now spans several technologies that differ in biological breadth, precision, specificity, sensitivity, cost, and method(s) of quantification; however, investigators currently lack an evidence-based framework to select or combine platforms. Here, we present the Atlas of Proteomic Technologies (APT) - a curated resource that evaluates six commercial platforms across ten analytical dimensions using published head-to-head evidence, expert evaluation, and iterative peer review. APT hosts two decision tools: the Help Me Choose tool maps a study's primary aim(s), scale, sample matrix, and technical constraints to a calibrated, weight-adjustable platform ranking, and the Help Me Combine tool ranks complementary platform pairs by their net-new protein coverage and user-specified technical priorities. Both tools were tested exhaustively across all possible combinations and behave in a balanced, merit-based manner. APT is openly accessible at https://aptatlas.org, providing downloadable tool specifications, seeded analysis scripts, and complete protein coverage lists, ensuring every score and recommendation is inspectable and reproducible.

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Whelan, C. D., Smith-Byrne, K.. 2026-09-16. Atlas of Proteomic Technologies: an evidence-based framework for selecting and combining commercial proteomics platforms. https://doi.org/10.64898/2026.09.10.750723

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