{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T14:52:57Z","timestamp":1783608777242,"version":"3.55.0"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T00:00:00Z","timestamp":1759968000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T00:00:00Z","timestamp":1759968000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Protoc"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1038\/s41596-025-01256-3","type":"journal-article","created":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:02:07Z","timestamp":1760025727000},"page":"2486-2510","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples"],"prefix":"10.1038","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3480-3421","authenticated-orcid":false,"given":"Zhen","family":"Dong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunlong","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9381-9848","authenticated-orcid":false,"given":"Wenhao","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7777-9468","authenticated-orcid":false,"given":"Kiryl D.","family":"Piatkevich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0429-0802","authenticated-orcid":false,"given":"Yi","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3869-7651","authenticated-orcid":false,"given":"Tiannan","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,10,9]]},"reference":[{"key":"1256_CR1","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1126\/science.1260088","volume":"347","author":"F Chen","year":"2015","unstructured":"Chen, F., Tillberg, P. W. & Boyden, E. S. Expansion microscopy. Science 347, 543\u2013548 (2015).","journal-title":"Science"},{"key":"1256_CR2","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.1038\/s41551-022-00912-3","volume":"6","author":"D Sarkar","year":"2022","unstructured":"Sarkar, D. et al. Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy. Nat. Biomed. Eng. 6, 1057\u20131073 (2022).","journal-title":"Nat. Biomed. Eng."},{"key":"1256_CR3","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1038\/nmeth.4261","volume":"14","author":"J-B Chang","year":"2017","unstructured":"Chang, J.-B. et al. Iterative expansion microscopy. Nat. Methods 14, 593\u2013599 (2017).","journal-title":"Nat. Methods"},{"key":"1256_CR4","doi-asserted-by":"publisher","first-page":"2128","DOI":"10.1038\/s41592-024-02454-9","volume":"21","author":"S Wang","year":"2024","unstructured":"Wang, S. et al. Single-shot 20-fold expansion microscopy. Nat. Methods 21, 2128\u20132134 (2024).","journal-title":"Nat. Methods"},{"key":"1256_CR5","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1038\/nbt.3625","volume":"34","author":"PW Tillberg","year":"2016","unstructured":"Tillberg, P. W. et al. Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. Nat. Biotechnol. 34, 987\u2013992 (2016).","journal-title":"Nat. Biotechnol."},{"key":"1256_CR6","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1038\/s41587-022-01546-1","volume":"41","author":"A Klimas","year":"2023","unstructured":"Klimas, A. et al. Magnify is a universal molecular anchoring strategy for expansion microscopy. Nat. Biotechnol. 41, 858\u2013869 (2023).","journal-title":"Nat. Biotechnol."},{"key":"1256_CR7","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1038\/s41592-023-01911-1","volume":"20","author":"Y Fan","year":"2023","unstructured":"Fan, Y. et al. Expansion spatial transcriptomics. Nat. Methods 20, 1179\u20131182 (2023).","journal-title":"Nat. Methods"},{"key":"1256_CR8","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-49384-w","volume":"15","author":"YH Chan","year":"2024","unstructured":"Chan, Y. H. et al. Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics. Nat. Commun. 15, 5036 (2024).","journal-title":"Nat. Commun."},{"key":"1256_CR9","doi-asserted-by":"publisher","DOI":"10.1016\/j.aca.2024.342345","volume":"1297","author":"L-C Chen","year":"2024","unstructured":"Chen, L.-C., Lee, C. & Hsu, C.-C. Towards developing a matrix-assisted laser desorption\/ionization mass spectrometry imaging (MALDI MSI) compatible tissue expansion protocol. Anal. Chim. Acta 1297, 342345 (2024).","journal-title":"Anal. Chim. Acta"},{"key":"1256_CR10","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-39616-w","volume":"14","author":"Y Bai","year":"2023","unstructured":"Bai, Y. et al. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat. Commun. 14, 4013 (2023).","journal-title":"Nat. Commun."},{"key":"1256_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-024-02431-9","author":"AH Shaib","year":"2024","unstructured":"Shaib, A. H. et al. One-step nanoscale expansion microscopy reveals individual protein shapes. Nat. Biotechnol. https:\/\/doi.org\/10.1038\/s41587-024-02431-9 (2024).","journal-title":"Nat. Biotechnol."},{"key":"1256_CR12","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1038\/s41587-022-01302-5","volume":"40","author":"A Mund","year":"2022","unstructured":"Mund, A. et al. Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat. Biotechnol. 40, 1231\u20131240 (2022).","journal-title":"Nat. Biotechnol."},{"key":"1256_CR13","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.1016\/j.cels.2023.10.003","volume":"14","author":"A Makhmut","year":"2023","unstructured":"Makhmut, A. et al. A framework for ultra-low-input spatial tissue proteomics. Cell Syst. 14, 1002\u20131014.e1005 (2023).","journal-title":"Cell Syst."},{"key":"1256_CR14","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1038\/s41592-023-02007-6","volume":"20","author":"FA Rosenberger","year":"2023","unstructured":"Rosenberger, F. A. et al. Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome. Nat. Methods 20, 1530\u20131536 (2023).","journal-title":"Nat. Methods"},{"key":"1256_CR15","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/s41586-024-08061-0","volume":"635","author":"TM Nordmann","year":"2024","unstructured":"Nordmann, T. M. et al. Spatial proteomics identifies JAKi as treatment for a lethal skin disease. Nature 635, 1001\u20131009 (2024).","journal-title":"Nature"},{"key":"1256_CR16","doi-asserted-by":"publisher","first-page":"2220","DOI":"10.1038\/s41592-024-02541-x","volume":"21","author":"TM Nordmann","year":"2024","unstructured":"Nordmann, T. M., Mund, A. & Mann, M. A new understanding of tissue biology from MS-based proteomics at single-cell resolution. Nat. Methods 21, 2220\u20132222 (2024).","journal-title":"Nat. Methods"},{"key":"1256_CR17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-53683-7","volume":"15","author":"Z Dong","year":"2024","unstructured":"Dong, Z. et al. Spatial proteomics of single cells and organelles on tissue slides using filter-aided expansion proteomics. Nat. Commun. 15, 9378 (2024).","journal-title":"Nat. Commun."},{"key":"1256_CR18","doi-asserted-by":"publisher","first-page":"12195","DOI":"10.1021\/acs.analchem.0c05372","volume":"93","author":"L Drelich","year":"2021","unstructured":"Drelich, L. et al. Toward high spatially resolved proteomics using expansion microscopy. Anal. Chem. 93, 12195\u201312203 (2021).","journal-title":"Anal. Chem."},{"key":"1256_CR19","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34824-2","volume":"13","author":"L Li","year":"2022","unstructured":"Li, L. et al. Spatially resolved proteomics via tissue expansion. Nat. Commun. 13, 7242 (2022).","journal-title":"Nat. Commun."},{"key":"1256_CR20","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/nmeth.1322","volume":"6","author":"JR Wi\u015bniewski","year":"2009","unstructured":"Wi\u015bniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359\u2013362 (2009).","journal-title":"Nat. Methods"},{"key":"1256_CR21","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-46777-9","volume":"15","author":"Z Ye","year":"2024","unstructured":"Ye, Z. et al. One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes. Nat. Commun. 15, 2474 (2024).","journal-title":"Nat. Commun."},{"key":"1256_CR22","doi-asserted-by":"publisher","first-page":"4864","DOI":"10.1021\/acs.analchem.6b00631","volume":"88","author":"W Chen","year":"2016","unstructured":"Chen, W. et al. Simple and integrated spintip-based technology applied for deep proteome profiling. Anal. Chem. 88, 4864\u20134871 (2016).","journal-title":"Anal. Chem."},{"key":"1256_CR23","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1038\/nbt.3892","volume":"35","author":"Y Zhao","year":"2017","unstructured":"Zhao, Y. et al. Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. Nat. Biotechnol. 35, 757\u2013764 (2017).","journal-title":"Nat. Biotechnol."},{"key":"1256_CR24","doi-asserted-by":"publisher","first-page":"1649","DOI":"10.1038\/s41596-020-0300-1","volume":"15","author":"O Bucur","year":"2020","unstructured":"Bucur, O. et al. Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. Nat. Protoc. 15, 1649\u20131672 (2020).","journal-title":"Nat. Protoc."},{"key":"1256_CR25","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1038\/s43586-021-00029-y","volume":"1","author":"JA Christopher","year":"2021","unstructured":"Christopher, J. A. et al. Subcellular proteomics. Nat. Rev. Methods Primers 1, 32 (2021).","journal-title":"Nat. Rev. Methods Primers"},{"key":"1256_CR26","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1038\/s41592-025-02664-9","volume":"22","author":"H Zhang","year":"2025","unstructured":"Zhang, H. et al. TEMI: tissue-expansion mass-spectrometry imaging. Nat. Methods 22, 1051\u20131058 (2025).","journal-title":"Nat. Methods"},{"key":"1256_CR27","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-53729-w","volume":"15","author":"J Kang","year":"2024","unstructured":"Kang, J. et al. Multiplexed expansion revealing for imaging multiprotein nanostructures in healthy and diseased brain. Nat. Commun. 15, 9722 (2024).","journal-title":"Nat. Commun."},{"key":"1256_CR28","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1038\/nbt.3641","volume":"34","author":"T Ku","year":"2016","unstructured":"Ku, T. et al. Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues. Nat. Biotechnol. 34, 973\u2013981 (2016).","journal-title":"Nat. Biotechnol."},{"key":"1256_CR29","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1038\/s41596-018-0117-3","volume":"14","author":"S Truckenbrodt","year":"2019","unstructured":"Truckenbrodt, S., Sommer, C., Rizzoli, S. O. & Danzl, J. G. A practical guide to optimization in X10 expansion microscopy. Nat. Protoc. 14, 832\u2013863 (2019).","journal-title":"Nat. Protoc."},{"key":"1256_CR30","doi-asserted-by":"publisher","first-page":"16733","DOI":"10.1021\/acs.analchem.3c03848","volume":"95","author":"H Chen","year":"2023","unstructured":"Chen, H. et al. Routine workflow of spatial proteomics on micro-formalin-fixed paraffin-embedded tissues. Anal. Chem. 95, 16733\u201316743 (2023).","journal-title":"Anal. Chem."},{"key":"1256_CR31","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1038\/s42003-021-01797-9","volume":"4","author":"C-F Tsai","year":"2021","unstructured":"Tsai, C.-F. et al. Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics. Commun. Biol. 4, 265 (2021).","journal-title":"Commun. Biol."},{"key":"1256_CR32","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"},{"key":"1256_CR33","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1083\/jcb.201004104","volume":"189","author":"M Linkert","year":"2010","unstructured":"Linkert, M. et al. Metadata matters: access to image data in the real world. J. Cell Biol. 189, 777\u2013782 (2010).","journal-title":"J. Cell Biol."},{"key":"1256_CR34","unstructured":"R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing https:\/\/www.R-project.org\/ (2024)."},{"key":"1256_CR35","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/nmeth.4256","volume":"14","author":"AT Kong","year":"2017","unstructured":"Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D. & Nesvizhskii, A. I. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat. Methods 14, 513\u2013520 (2017).","journal-title":"Nat. Methods"},{"key":"1256_CR36","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1074\/mcp.TIR120.002048","volume":"19","author":"F Yu","year":"2020","unstructured":"Yu, F. et al. Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol. Cell. Proteom. 19, 1575\u20131585 (2020).","journal-title":"Mol. Cell. Proteom."},{"key":"1256_CR37","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","volume":"17","author":"V Demichev","year":"2020","unstructured":"Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S. & Ralser, M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat. Methods 17, 41\u201344 (2020).","journal-title":"Nat. Methods"},{"key":"1256_CR38","doi-asserted-by":"publisher","first-page":"3944","DOI":"10.1038\/s41467-022-31492-0","volume":"13","author":"V Demichev","year":"2022","unstructured":"Demichev, V. et al. dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nat. Commun. 13, 3944 (2022).","journal-title":"Nat. Commun."},{"key":"1256_CR39","doi-asserted-by":"publisher","first-page":"5483","DOI":"10.1007\/s00216-022-03944-5","volume":"414","author":"AG Bury","year":"2022","unstructured":"Bury, A. G. et al. A subcellular cookie cutter for spatial genomics in human tissue. Anal. Bioanal. Chem. 414, 5483\u20135492 (2022).","journal-title":"Anal. Bioanal. Chem."},{"key":"1256_CR40","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","volume":"50","author":"Y Perez-Riverol","year":"2021","unstructured":"Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543\u2013D552 (2021).","journal-title":"Nucleic Acids Res."},{"key":"1256_CR41","doi-asserted-by":"publisher","unstructured":"Wenhhao & ZhenDongWL. Wenhhao\/FAXP: Version 1.0.3. Zenodo https:\/\/doi.org\/10.5281\/zenodo.13843661 (2025).","DOI":"10.5281\/zenodo.13843661"}],"container-title":["Nature Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41596-025-01256-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41596-025-01256-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41596-025-01256-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T14:01:46Z","timestamp":1781100106000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41596-025-01256-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,9]]},"references-count":41,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["1256"],"URL":"https:\/\/doi.org\/10.1038\/s41596-025-01256-3","relation":{},"ISSN":["1754-2189","1750-2799"],"issn-type":[{"value":"1754-2189","type":"print"},{"value":"1750-2799","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,9]]},"assertion":[{"value":"17 January 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 July 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"T.G. and Y.Z. are shareholders of Westlake Omics Biotechnology. T.G., Z.D., Y.Z., C.W. and K.D.P. are listed as inventors on a granted patent (Chinese patent no. ZL 202310889444.4) submitted by the Westlake Laboratory of Life Sciences and Biomedicine, which pertains to the FAXP methods. All other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}