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However, LiP-MS-based proteomics data analysis is fundamentally different from that of conventional proteomics informatics. LiP-MS relies on peptide-centric analysis in order to pinpoint structural regions or residues within a protein that exhibit conformational changes. The presence of a large number of semitryptic peptides substantially increases LiP-MS data complexity. Moreover, there is a lack of consensus on the statistical criteria for defining structural changes. To 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 a 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 reanalysis 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.<\/jats:p>","DOI":"10.1021\/acs.analchem.6c02411","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T12:08:01Z","timestamp":1784203681000},"page":"21634-21649","source":"Crossref","is-referenced-by-count":0,"title":["Evaluating\nDIA LiP-MS Analysis Workflows with a Hybrid\nLiP Proteome Benchmark"],"prefix":"10.1021","volume":"98","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5472-7772","authenticated-orcid":true,"given":"Shanshan","family":"Li","sequence":"first","affiliation":[{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2008-9933","authenticated-orcid":true,"given":"Shijia","family":"Yuan","sequence":"additional","affiliation":[{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiting","family":"Luo","sequence":"additional","affiliation":[{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingyi","family":"Xu","sequence":"additional","affiliation":[{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaoyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronghui","family":"Lou","sequence":"additional","affiliation":[{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hebin","family":"Liu","sequence":"additional","affiliation":[{"name":"Shanghai Omicsolution Co., Ltd , ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengpin","family":"Shen","sequence":"additional","affiliation":[{"name":"Shanghai Omicsolution Co., Ltd , ,","place":["Shanghai, China, 200240"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5245-2477","authenticated-orcid":true,"given":"Wenqing","family":"Shui","sequence":"additional","affiliation":[{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]},{"name":"ShanghaiTech University , , ,","place":["Shanghai, China, 201210"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"issue":"10","key":"2026072808080541400_cit1","doi-asserted-by":"publisher","first-page":"1036","DOI":"10.1038\/nbt.2999","article-title":"Global analysis of protein structural changes in complex\nproteomes","volume":"32","author":"Feng","year":"2014","journal-title":"Nat. Biotechnol."},{"issue":"29","key":"2026072808080541400_cit2","doi-asserted-by":"publisher","first-page":"20045","DOI":"10.1021\/jacs.4c03922","article-title":"Structural Mass Spectrometry\nCaptures Residue-Resolved Comprehensive Conformational Rearrangements\nof a G Protein-Coupled Receptor","volume":"146","author":"Liu","year":"2024","journal-title":"J. Am. Chem.\nSoc."},{"issue":"3","key":"2026072808080541400_cit3","doi-asserted-by":"publisher","first-page":"1513","DOI":"10.1038\/s44319-024-00076-y","article-title":"Regulatory\nsites of CaM-sensitive adenylyl cyclase AC8 revealed by cryo-EM and\nstructural proteomics","volume":"25","author":"Khanppnavar","year":"2024","journal-title":"EMBO Rep"},{"key":"2026072808080541400_cit4","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/s44320-025-00182-6","article-title":"Limited proteolysis-coupled mass\nspectrometry captures proteome-wide protein structural alterations\nand biomolecular condensation in living cells","volume":"22","author":"Elsa\u0308sser","year":"2026","journal-title":"Mol. Syst. 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Biol."},{"issue":"1","key":"2026072808080541400_cit12","doi-asserted-by":"publisher","DOI":"10.3390\/cells10010068","article-title":"Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol\n4,5-Bisphosphate Effectors in Human Nuclear Proteome","volume":"10","author":"Sztacho","year":"2021","journal-title":"Cells"},{"issue":"3","key":"2026072808080541400_cit13","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1016\/j.cell.2016.09.031","article-title":"L-Arginine Modulates T Cell Metabolism and Enhances\nSurvival and Anti-tumor Activity","volume":"167","author":"Geiger","year":"2016","journal-title":"Cell"},{"issue":"11","key":"2026072808080541400_cit14","doi-asserted-by":"publisher","first-page":"2391","DOI":"10.1038\/nprot.2017.100","article-title":"Measuring protein structural\nchanges on a proteome-wide scale using limited proteolysis-coupled\nmass spectrometry","volume":"12","author":"Schopper","year":"2017","journal-title":"Nat. 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Adv."},{"key":"2026072808080541400_cit40","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2022.964295","article-title":"Drug affinity-responsive\ntarget stability\nunveils filamins as biological targets for artemetin, an anti-cancer\nflavonoid","volume":"9","author":"Ferraro","year":"2022","journal-title":"Front. Mol. Biosci."},{"issue":"26","key":"2026072808080541400_cit41","doi-asserted-by":"publisher","first-page":"9746","DOI":"10.1021\/acs.analchem.2c05731","article-title":"DiLeu Isobaric Labeling Coupled with Limited Proteolysis Mass Spectrometry\nfor High-Throughput Profiling of Protein Structural Changes in Alzheimer\u2019s\nDisease","volume":"95","author":"Lu","year":"2023","journal-title":"Anal. 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