GROQ-seq Enables Cross-site Reproducibility for High-Throughput Measurement of Protein Function

Published

March 31, 2026

Author(s)

Aviv Spinner, Amanda Reider Apel, David Ross, Svetlana Ikonomova, Dana Cortade, Catherine Baranowski, Andi Dhroso, Kristen Sheldon, Courtney Tretheway, Erika DeBenedictis, Corey Hudson

Abstract

High-throughput functional assays are increasingly used to generate large-scale protein function datasets for protein engineering and machine learning applications. However, the utility of such datasets depends on the reproducibility of the underlying measurements. Here we report reproducible, quantitative measurements of protein sequence-to-function data at scale across two facilities. We analyze GROQ-seq (Growth-based Quantitative Sequencing) measurements of three bacterial transcription factors. Independent barcode measurements of the same sequence produce highly consistent functional estimates, demonstrating strong biological reproducibility (across all transcription factors the mean Root Mean Square Deviation [RMSD] ≈ 0.53 and mean Spearman ≈ 0.63). We also compared experiments performed at two facilities using a shared protocol, but with differing levels of automation and system integration. We observe strong agreement between measurements taken at the two sites (mean RMSD ≈ 0.41 and mean Spearman ≈ 0.73). Additionally, data from the two facilities consistently identify the same high-functioning variants. Together, these results demonstrate that GROQ-seq enables reproducible, scalable measurement of protein function suitable for large, aggregated datasets.

Citation

biorxiv.org

Pub Weblink

https://www.biorxiv.org/

Pub Type

Websites

Keywords

Deep Mutational Scanning, Protein Sequence-Function Relationships, AI-Ready Biological Data

Citation

Spinner, A. , Reider Apel, A. , Ross, D. , Ikonomova, S. , Cortade, D. , Baranowski, C. , Dhroso, A. , Sheldon, K. , Tretheway, C. , DeBenedictis, E. and Hudson, C. (2026), GROQ-seq Enables Cross-site Reproducibility for High-Throughput Measurement of Protein Function, biorxiv.org, [online], https://www.biorxiv.org/ (Accessed April 1, 2026)