iProXProteomicsWenqing ShuiHomo Sapienshttp://www.iprox.org/page/project.html?id=IPX0016563000shuiwq@shanghaitech.edu.cnShanghaiTech UniversityiProXfalseLiP-MS data analysis workflows with a hybrid LiP proteome benchmarkTo evaluate informatics workflows for DIA-based LiP-MS, we generated a high-quality benchmark data set comprising more than 170,000 LiP peptides with defined composition. We then performed comprehensive assessment of major DIA analysis platforms incorporating different spectral libraries, and introduced DIA-LiPQuan, an informatics pipeline tailored to DIA LiP-MS quantification and downstream analysis. Data re-analysis by DIA-LiPQuan with in silico libraries allows sensitive and robust detection of both site-specific structural remodeling of proteins and drug-bound protein targets from the cellular proteome. Collectively, our study provides a valuable benchmark resource and informatics package for LiP-MS data mining, which would facilitate its broader applications in structural proteomics and drug discovery.Tue Apr 14 00:00:00 BST 2026PXD0771719606