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

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.