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C. Wong Magna Fund in Ningbo University","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/501100020738","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/na","name":"Ningbo Top Talent Project","doi-asserted-by":"publisher","award":["215-432094250"],"award-info":[{"award-number":["215-432094250"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cross-linking mass spectrometry (XL-MS) has emerged as an indispensable tool for dissecting protein conformations and protein\u2013protein interactions (PPIs) within native biological systems. However, conventional in vivo XL-MS workflows suffer from significant sample loss during sample preparation, necessitating large input quantities of the starting material and fundamentally limiting their widespread applicability to mass-limited samples. Herein, we report the development of a tandem MICROFASP platform that uniquely integrates in vivo chemical cross-linking with seamless in situ sample preparation to drastically minimize sample loss throughout the entire workflow. Using disuccinimidyl suberate (DSS) as a model cross-linker, we systematically optimized all critical experimental parameters, including cross-linking reaction duration, lysis buffer formulation, and mass spectrometry data acquisition conditions. Without any pre-enrichment, we identified 517 intercross-linked peptides from just 10,000 K562 cells, a 3.5-fold increase relative to the state-of-the-art result with enrichment reported to date. Notably, 318 cross-linked peptides were identified from only 2500 living K562 cells. Structural mapping and PPI network analysis confirmed the validity of the identified cross-links, with over 97% of the cross-linked sites falling within the distance constraint of the DSS. This tandem MICROFASP method resolves the long-standing sensitivity limitation of in vivo XL-MS in low-cell-number samples, paving the way for systematic analysis of protein conformations and dynamic PPIs in clinical biopsies and the tumor microenvironment.<\/jats:p>","DOI":"10.1021\/acs.analchem.6c01538","type":"journal-article","created":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T20:43:41Z","timestamp":1784321021000},"page":"22132-22141","source":"Crossref","is-referenced-by-count":0,"title":["Tandem MICROFASP\nMethod-Enabled High-Sensitivity In\nVivo Cross-Linking Mass Spectrometry Analysis of Low-Cell-Number Samples\nwithout Enrichment"],"prefix":"10.1021","volume":"98","author":[{"given":"Yu","family":"He","sequence":"first","affiliation":[{"name":"Ningbo University , , , ,","place":["Ningbo, Zhejiang, China, 315211"]},{"name":"Ningbo University , , ,","place":["Ningbo, China, 315211"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8280-5284","authenticated-orcid":true,"given":"Yang","family":"Li","sequence":"additional","affiliation":[{"name":"Ningbo University , , , ,","place":["Ningbo, Zhejiang, China, 315211"]},{"name":"Ningbo University , , ,","place":["Ningbo, China, 315211"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-9733-0365","authenticated-orcid":true,"given":"Rong","family":"Liu","sequence":"additional","affiliation":[{"name":"Ningbo University , , ,","place":["Ningbo, China, 315211"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keqi","family":"Tang","sequence":"additional","affiliation":[{"name":"Ningbo University , , ,","place":["Ningbo, China, 315211"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengyan","family":"Hu","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Center for Disease Control and Prevention , , ,","place":["Hangzhou, Zhejiang, China, 310051"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8617-6386","authenticated-orcid":true,"given":"Zhenbin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Ningbo University , , , ,","place":["Ningbo, Zhejiang, China, 315211"]},{"name":"Ningbo University , , ,","place":["Ningbo, China, 315211"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,17]]},"reference":[{"issue":"6","key":"2026080408073999300_cit1","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1002\/anie.201409336","article-title":"Krebs Cycle\nMetabolon: Structural Evidence of Substrate\nChanneling Revealed by Cross-Linking and Mass Spectrometry","volume":"54","author":"Wu","year":"2015","journal-title":"Angew. 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Proteome Res."},{"issue":"1","key":"2026080408073999300_cit9","doi-asserted-by":"publisher","first-page":"3404","DOI":"10.1038\/s41467-019-11337-z","article-title":"A high-speed search\nengine pLink\n2 with systematic evaluation for proteome-scale identification of\ncross-linked peptides","volume":"10","author":"Chen","year":"2019","journal-title":"Nat. Commun."},{"issue":"1","key":"2026080408073999300_cit10","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1038\/s42004-024-01386-x","article-title":"Proteome-wide non-cleavable crosslink\nidentification with MS Annika 3.0 reveals the structure of the C.\nelegans Box C\/D complex","volume":"7","author":"Birklbauer","year":"2024","journal-title":"Commun. 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Mass Spectrom."},{"issue":"28","key":"2026080408073999300_cit25","doi-asserted-by":"publisher","first-page":"10670","DOI":"10.1021\/acs.analchem.3c01369","article-title":"Progress\ntoward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization\nof Protein Structures and Networks In Vivo","volume":"95","author":"Faustino","year":"2023","journal-title":"Anal. Chem."},{"issue":"30","key":"2026080408073999300_cit26","doi-asserted-by":"publisher","first-page":"12341","DOI":"10.1021\/acs.analchem.4c01600","article-title":"An Optimized Miniaturized Filter-Aided Sample Preparation Method\nfor Sensitive Cross-Linking Mass Spectrometry Analysis of Microscale\nSamples","volume":"96","author":"He","year":"2024","journal-title":"Anal. 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Chem."},{"issue":"W1","key":"2026080408073999300_cit28","doi-asserted-by":"publisher","first-page":"W216","DOI":"10.1093\/nar\/gkac194","article-title":"DAVID: a web server for functional\nenrichment analysis and functional annotation of gene lists (2021\nupdate)","volume":"50","author":"Sherman","year":"2022","journal-title":"Nucleic Acids Res."},{"issue":"D1","key":"2026080408073999300_cit29","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: protein\u2013protein\nassociation networks with increased coverage, supporting functional\ndiscovery in genome-wide experimental datasets","volume":"47","author":"Szklarczyk","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"10","key":"2026080408073999300_cit30","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1107\/S0907444912027047","article-title":"Structures\nof bovine, equine and leporine serum albumin","volume":"68","author":"Bujacz","year":"2012","journal-title":"Acta Crystallogr., Sect. 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