Nature Methods最新文献

{"title":"A universal language for finding mass spectrometry data patterns.","authors":"Tito Damiani, Alan K Jarmusch, Allegra T Aron, Daniel Petras, Vanessa V Phelan, Haoqi Nina Zhao, Wout Bittremieux, Deepa D Acharya, Mohammed M A Ahmed, Anelize Bauermeister, Matthew J Bertin, Paul D Boudreau, Ricardo M Borges, Benjamin P Bowen, Christopher J Brown, Fernanda O Chagas, Kenneth D Clevenger, Mario S P Correia, William J Crandall, Max Crüsemann, Eoin Fahy, Oliver Fiehn, Neha Garg, William H Gerwick, Jeffrey R Gilbert, Daniel Globisch, Paulo Wender P Gomes, Steffen Heuckeroth, C Andrew James, Scott A Jarmusch, Sarvar A Kakhkhorov, Kyo Bin Kang, Nikolas Kessler, Roland D Kersten, Hyunwoo Kim, Riley D Kirk, Oliver Kohlbacher, Eftychia E Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T Luu, Tal Luzzatto Knaan, Helena Mannochio-Russo, Michael T Marty, Yuki Matsuzawa, Andrew C McAvoy, Laura-Isobel McCall, Osama G Mohamed, Omri Nahor, Heiko Neuweger, Timo H J Niedermeyer, Kozo Nishida, Trent R Northen, Kirsten E Overdahl, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T Sachsenberg, Laura M Sanchez, Robin Schmid, Cole Stevens, Shankar Subramaniam, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Justin J J van der Hooft, Andrea Vicini, Axel Walter, Tilmann Weber, Quanbo Xiong, Tao Xu, Tomáš Pluskal, Pieter C Dorrestein, Mingxun Wang","doi":"10.1038/s41592-025-02660-z","DOIUrl":"10.1038/s41592-025-02660-z","url":null,"abstract":"<p><p>Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1247-1254"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells.","authors":"Patrick J Nugent, Heungwon Park, Cynthia L Wladyka, James N Yelland, Sayantani Sinha, Katharine Y Chen, Christine Bynum, Grace Quarterman, Stanley C Lee, Andrew C Hsieh, Arvind Rasi Subramaniam","doi":"10.1038/s41592-025-02702-6","DOIUrl":"10.1038/s41592-025-02702-6","url":null,"abstract":"<p><p>RNAs undergo a complex choreography of metabolic processes that are regulated by thousands of RNA-associated proteins. Here we introduce ReLiC, a scalable and high-throughput RNA-linked CRISPR approach to measure the responses of diverse RNA metabolic processes to knockout of 2,092 human genes encoding all known RNA-associated proteins. ReLiC relies on an iterative strategy to integrate genes encoding Cas9, single-guide RNAs (sgRNAs) and barcoded reporter libraries into a defined genomic locus. Combining ReLiC with polysome fractionation reveals key regulators of ribosome occupancy, uncovering links between translation and proteostasis. Isoform-specific ReLiC captures differential regulation of intron retention and exon skipping by SF3B complex subunits. Chemogenomic ReLiC screens decipher translational regulators upstream of messenger RNA (mRNA) decay and identify a role for the ribosome collision sensor GCN1 during treatment with the anti-leukemic drug homoharringtonine. Our work demonstrates ReLiC as a powerful framework for discovering and dissecting post-transcriptional regulatory networks in human cells.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1237-1246"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A highly stable monomeric red fluorescent protein for advanced microscopy.","authors":"Haiyan Xiong, Qiyuan Chang, Jiayi Ding, Shuyuan Wang, Wenhao Zhang, Yu Li, Yaochen Wu, Pengyan Lin, Chengyu Yang, Miaoxing Liu, Guicun Fang, Yiwei Yang, Jiongfang Xie, Dong Qi, Tao Jiang, Wenfeng Fu, Fen Hu, Yiming Chen, Rongcai Yue, Yanbin Li, Yong Cui, Min Li, Shilong Fan, Yufeng Yang, Yunlu Xu, Dong Li, Fenghua Zhang, Hu Zhao, Congxian Wu, Qingbing Zheng, Kiryl D Piatkevich, Zhifei Fu","doi":"10.1038/s41592-025-02676-5","DOIUrl":"10.1038/s41592-025-02676-5","url":null,"abstract":"<p><p>The stability of fluorescent proteins (FPs) is crucial for imaging techniques such as live-cell imaging, super-resolution microscopy and correlative light and electron microscopy. Although stable green and yellow FPs are available, stable monomeric red FPs (RFPs) remain limited. Here we develop an extremely stable monomeric RFP named mScarlet3-H and determine its structure at a 1.5 Å resolution. mScarlet3-H exhibits remarkable resistance to high temperature, chaotropic conditions and oxidative environments, enabling efficient correlative light and electron microscopy imaging and rapid (less than 1 day) whole-organ tissue clearing. In addition, its high photostability allows long-term three-dimensional structured illumination microscopy imaging of mitochondrial dynamics with minimal photobleaching. It also facilitates dual-color live-cell stimulated emission depletion imaging with a high signal-to-noise ratio and strong specificity. Systematic benchmarking against high-performing RFPs established mScarlet3-H as a highly stable RFP for multimodality microscopy in cell cultures and model organisms, complementing green FPs for multiplexed imaging in zebrafish, mice and Nicotiana benthamiana.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1288-1298"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridge to a brighter future in fluorescence imaging.","authors":"Frederik Brøndsted, Lei G Wang","doi":"10.1038/s41592-025-02695-2","DOIUrl":"10.1038/s41592-025-02695-2","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1137-1139"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Confronting the challenge of cell segmentation in spatial transcriptomics.","authors":"","doi":"10.1038/s41592-025-02717-z","DOIUrl":"10.1038/s41592-025-02717-z","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1150-1151"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acoustic sectioning for volumetric imaging.","authors":"Rita Strack","doi":"10.1038/s41592-025-02736-w","DOIUrl":"10.1038/s41592-025-02736-w","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1129"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ring deconvolution microscopy: exploiting symmetry for efficient spatially varying aberration correction.","authors":"Amit Kohli, Anastasios N Angelopoulos, David McAllister, Esther Whang, Sixian You, Kyrollos Yanny, Federico M Gasparoli, Bo-Jui Chang, Reto Fiolka, Laura Waller","doi":"10.1038/s41592-025-02684-5","DOIUrl":"10.1038/s41592-025-02684-5","url":null,"abstract":"<p><p>The most ubiquitous form of aberration correction for microscopy is deconvolution; however, deconvolution relies on the assumption that the system's point spread function is the same across the entire field of view. This assumption is often inadequate, but space-variant deblurring techniques generally require impractical amounts of calibration and computation. We present an imaging pipeline that leverages symmetry to provide simple and fast spatially varying deblurring. Our ring deconvolution microscopy method utilizes the rotational symmetry of most microscopes and cameras, and naturally extends to sheet deconvolution in the case of lateral symmetry. We derive theory and algorithms for ring deconvolution microscopy and propose a neural network based on Seidel aberration coefficients as a fast alternative. We demonstrate improvements in speed and image quality as compared to standard deconvolution and existing spatially varying deblurring across a diverse range of microscope modalities, including miniature microscopy, multicolor fluorescence microscopy, multimode fiber micro-endoscopy and light-sheet fluorescence microscopy. Our approach enables near-isotropic, subcellular resolution in each of these applications.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1311-1320"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A telescopic microscope equipped with a quanta image sensor for live-cell bioluminescence imaging.","authors":"Ruyu Ma, Luciano M Santino, Tomáš Chobola, Niklas Armbrust, Julian Geilenkeuser, Sapthagiri Sukumaran, Zhizi Jing, Anastasia Levkina, Korneel Ridderbeek, Tingying Peng, Dong-Jiunn Jeffery Truong, Sebastian Doll, Gil Gregor Westmeyer, Jian Cui","doi":"10.1038/s41592-025-02694-3","DOIUrl":"10.1038/s41592-025-02694-3","url":null,"abstract":"<p><p>Bioluminescence is an attractive alternative to fluorescence for live-cell imaging; however, its low intensity has prevented widespread adoption. Specialized microscopes compensate by sacrificing spatial resolution, field of view and dynamic range-constraints imposed by the highest-sensitivity camera to date: the electron-multiplying charge-coupled device. Recently, quanta image sensor (QIS) technology has emerged for low-light imaging. Here, we show that a commercial QIS camera has exceptional sensitivity; however, its sensor dimensions necessitate a microscope designed to maximize its properties. We introduce a Keplerian-telescope-inspired microscope setup that, with the QIS, results in modestly improved signal-to-noise ratios at substantially higher spatial resolution, field of view and dynamic range, relative to the state of the art. The telescopic design also confers modularity, enabling multimodal imaging with epifluorescence. The 'QIScope' makes bioluminescence a viable tool for technically challenging live-cell experiments such as monitoring intracellular and extracellular vesicles simultaneously and the dynamics of low-abundance proteins.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1321-1330"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165864/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crediting early-career researchers in peer review.","authors":"","doi":"10.1038/s41592-025-02738-8","DOIUrl":"10.1038/s41592-025-02738-8","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1121-1122"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Empowering chemists to mine high-throughput mass spectrometry datasets.","authors":"","doi":"10.1038/s41592-025-02661-y","DOIUrl":"10.1038/s41592-025-02661-y","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1146-1147"},"PeriodicalIF":36.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}