2026/06/08 by Louisa Grauvogel, Elisabeth Zollbrecht, Tim Heymann +4 · 1 voice
Chemistry · Biochemistry, Genetics and Molecular Biology · #Advanced Proteomics Techniques and Applications #Biotin and Related Studies #Bioinformatics and Genomic Networks
paper · doi:10.64898/2026.06.03.729763
Abstract Although protein-protein interactions govern virtually all cellular processes, systematic interactome mapping by affinity enrichment mass spectrometry (AE-MS) is constrained by manual sample preparation and lengthy liquid chromatography (LC)-MS/MS acquisition. Here we present High-throughput Interactome Profiling by MS (HIP-MS), an automated, end-to-end pipeline that overcomes these limitations. It leverages the compact, high-affinity ALFA tag for on-plate nanobody capture in 384-well format, combined with on-plate tryptic digestion. It can process almost 10,000 samples per week from protein expression up to MS measurement and can be combined with ultra-fast gradient LC-MS acquisition of 500 samples per day. HIP-MS remains sensitive down to low-microgram lysate inputs, a 4,000-fold reduction compared to recent large-scale screens. Our pipeline recovers complexes from diverse cellular compartments and resolves endogenous membrane receptor signaling. HIP-MS establishes a scalable foundation for systematic interrogation of protein interactions across conditions, perturbations, and time, and for the generation of large-scale datasets for computational modeling.