Advancing DIA-Based Limited Proteolysis Workflows: Introducing DIA-LiPA.

ABSTRACT: Limited proteolysis coupled to mass spectrometry (LiP-MS) probes protein conformational dynamics, but interpretation of LiP-MS data is complicated by heterogeneous proteolytic cleavage patterns and missing data. Recent advances in data-independent acquisition (DIA) and machine learning-based search engines promise improved sensitivity and reproducibility, yet their performance in LiP-MS workflows remains underexplored. We systematically evaluated selected library-free DIA workflows using a rapamycin-treated human cell lysate and a yeast heat shock data set, benchmarking DIA-NN and Spectronaut for identification depth, reproducibility, and false discovery rate control. Our results show that library-free approaches achieve high sensitivity, eliminating the experimental overhead and sample re

SUBMITTER: Van Leene C 

PROVIDER: S-EPMC12937052 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature