Nature Protocols Nature Protocols is an interactive online resource for laboratory protocols, providing step-by-step instructions for using and adapting research techniques that users can take straight to the lab bench and apply in their own research. Protocols are commissioned by the editorial team from leading laboratories. They are edited and peer-reviewed to ensure the highest level of quality and reproducibility. All protocols must have been proven to work, having been used to acquire data in published research papers. The focus is on providing practical information that is not available in research papers, such as explaining the critical points in the procedure, anticipated results (what to expect if the experiment has worked) and how to troubleshoot problems. Nature Protocols publishes protocols used to answer outstanding biological and biomedical research questions, including methods grounded in physics and chemistry that can be applied to biological problems. Protocols are added weekly and cover new methods, as well as classic, wellestablished techniques. Protocols are fully searchable online and also available in print on demand. http://feeds.nature.com/nprot/rss/current Nature Publishing Group en © 2025 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Nature Protocols © 2025 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. [email protected]
  • Nature Protocols https://www.nature.com/uploads/product/nprot/rss.PNG http://feeds.nature.com/nprot/rss/current <![CDATA[Comparing methods for preparing slippery liquid-like polydimethylsiloxane coatings]]> https://www.nature.com/articles/s41596-025-01253-6 <![CDATA[
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    Nature Protocols, Published online: 28 October 2025; doi:10.1038/s41596-025-01253-6

    Slippery covalently attached liquid surfaces are useful in many applications that require low-static friction to droplets. This review compares six prominent methods for preparing polydimethylsiloxane bound to silica surfaces and highlights pitfalls and time savers.]]> <![CDATA[Comparing methods for preparing slippery liquid-like polydimethylsiloxane coatings]]> Isaac J. GreshamHernán Barrio-ZhangJae Hyung ChoBehrooz KhatirGary G. WellsKevin GolovinGlen McHaleChiara Neto doi:10.1038/s41596-025-01253-6 Nature Protocols, Published online: 2025-10-28; | doi:10.1038/s41596-025-01253-6 2025-10-28 Nature Protocols 10.1038/s41596-025-01253-6 https://www.nature.com/articles/s41596-025-01253-6 <![CDATA[Publisher Correction: NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns]]> https://www.nature.com/articles/s41596-025-01297-8 <![CDATA[

    Nature Protocols, Published online: 16 October 2025; doi:10.1038/s41596-025-01297-8

    Publisher Correction: NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns]]>     <![CDATA[Publisher Correction: NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns]]> Asmaa SamyCheng Yong ThamMatthew DyerTouati Benoukraf doi:10.1038/s41596-025-01297-8 Nature Protocols, Published online: 2025-10-16; | doi:10.1038/s41596-025-01297-8 2025-10-16 Nature Protocols 10.1038/s41596-025-01297-8 https://www.nature.com/articles/s41596-025-01297-8     <![CDATA[Navigating the data processing for cytometry-based single-cell proteomics]]> https://www.nature.com/articles/s41596-025-01257-2 <![CDATA[

    Nature Protocols, Published online: 16 October 2025; doi:10.1038/s41596-025-01257-2

    ANPELA is a software package to compare and assess the performance of different workflows for processing single-cell proteomic data, ensuring the user selects the most appropriate processing workflow for their experimental design question.]]>     <![CDATA[Navigating the data processing for cytometry-based single-cell proteomics]]> Huaicheng SunYuan ZhouRuoyu JiangYuxuan LiuChengbin GuZiqi PanMinjie MouXichen LianBohan ChenTianle NiuYing ZhangYintao ZhangBaoliang ZhangXiuna SunHao YangXin ShenYangbo DaiJiannan DengSiqi LiuYang ZhangMang XiaoWanqing XieQingxia YangTingting FuFeng Zhu doi:10.1038/s41596-025-01257-2 Nature Protocols, Published online: 2025-10-16; | doi:10.1038/s41596-025-01257-2 2025-10-16 Nature Protocols 10.1038/s41596-025-01257-2 https://www.nature.com/articles/s41596-025-01257-2     <![CDATA[Sonicated inks and focused-ultrasound writing enable deep-penetration acoustic volumetric printing]]> https://www.nature.com/articles/s41596-025-01258-1 <![CDATA[

    Nature Protocols, Published online: 15 October 2025; doi:10.1038/s41596-025-01258-1

    The preparation of multicomponent viscoelastic self-enhancing sono-inks, synthesized as phase-transition reversible acoustic absorbers, enables acoustic volumetric printing beneath diverse tissue types in optically scattering media.]]>     <![CDATA[Sonicated inks and focused-ultrasound writing enable deep-penetration acoustic volumetric printing]]> Xiao KuangQiangzhou RongSaud BelalNanchao WangTri VuAbigail Herrera-RuizZebang ZhangYu Shrike ZhangJunjie Yao doi:10.1038/s41596-025-01258-1 Nature Protocols, Published online: 2025-10-15; | doi:10.1038/s41596-025-01258-1 2025-10-15 Nature Protocols 10.1038/s41596-025-01258-1 https://www.nature.com/articles/s41596-025-01258-1     <![CDATA[Best practice mass photometry: a guide to optimal single-molecule mass measurement]]> https://www.nature.com/articles/s41596-025-01255-4 <![CDATA[

    Nature Protocols, Published online: 13 October 2025; doi:10.1038/s41596-025-01255-4

    In mass photometry, the optical contrast generated by individual molecules at a glass–water interface enables mass-resolved quantification of biomolecular mixtures. This protocol describes how to optimize and validate this method.]]>     <![CDATA[Best practice mass photometry: a guide to optimal single-molecule mass measurement]]> Jiří KratochvílRaman van WeeJan Christoph ThieleDan LoewenthalJack BardzilKishwar IqbalJustin L. P. BeneschStephen ThorpePhilipp Kukura doi:10.1038/s41596-025-01255-4 Nature Protocols, Published online: 2025-10-13; | doi:10.1038/s41596-025-01255-4 2025-10-13 Nature Protocols 10.1038/s41596-025-01255-4 https://www.nature.com/articles/s41596-025-01255-4     <![CDATA[Manufacturing synthetic viscoelastic antigen-presenting cells for immunotherapy]]> https://www.nature.com/articles/s41596-025-01265-2 <![CDATA[

    Nature Protocols, Published online: 09 October 2025; doi:10.1038/s41596-025-01265-2

    Protocol for fabricating synthetic viscoelastic antigen-presenting cells and their application in T cell engineering. These synthetic cells support robust T cell activation and expansion and improve chimeric antigen receptor transduction efficiency.]]>     <![CDATA[Manufacturing synthetic viscoelastic antigen-presenting cells for immunotherapy]]> Zeyang LiuYan-Ruide LiYoucheng YangEnbo ZhuHaochen NanYue YanBo ZhangGuorui ChenNicolas PedroncelliZibai LyuJason LinJennifer SotoLili YangSong Li doi:10.1038/s41596-025-01265-2 Nature Protocols, Published online: 2025-10-09; | doi:10.1038/s41596-025-01265-2 2025-10-09 Nature Protocols 10.1038/s41596-025-01265-2 https://www.nature.com/articles/s41596-025-01265-2     <![CDATA[Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples]]> https://www.nature.com/articles/s41596-025-01256-3 <![CDATA[

    Nature Protocols, Published online: 09 October 2025; doi:10.1038/s41596-025-01256-3

    Filter-aided expansion proteomics facilitates spatial proteomics at subcellular resolution by integrating tissue expansion, imaging-guided microdissection and filter-aided in-gel digestion. This combination enhances the resolution, throughput and reproducibility for data-independent acquisition-based mass spectrometry analysis.]]>     <![CDATA[Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples]]> Zhen DongChunlong WuJiayi ChenWenhao JiangKiryl D. PiatkevichYi ZhuTiannan Guo doi:10.1038/s41596-025-01256-3 Nature Protocols, Published online: 2025-10-09; | doi:10.1038/s41596-025-01256-3 2025-10-09 Nature Protocols 10.1038/s41596-025-01256-3 https://www.nature.com/articles/s41596-025-01256-3     <![CDATA[Microfluidic gradients create a stem cell model of the human central nervous system]]> https://www.nature.com/articles/s41596-025-01269-y <![CDATA[

    Nature Protocols, Published online: 08 October 2025; doi:10.1038/s41596-025-01269-y

    The complex spatiotemporal signaling of human neural tube development is successfully engineered in a device using microfluidic gradients, creating a high-fidelity model of the developing human central nervous system.]]>     <![CDATA[Microfluidic gradients create a stem cell model of the human central nervous system]]> Peter SerlesGiorgia Quadrato doi:10.1038/s41596-025-01269-y Nature Protocols, Published online: 2025-10-08; | doi:10.1038/s41596-025-01269-y 2025-10-08 Nature Protocols 10.1038/s41596-025-01269-y https://www.nature.com/articles/s41596-025-01269-y