Nature Methods最新文献_第9页

Influence of different sample preparation approaches on proteoform identification by top-down proteomics 不同样品制备方法对自上而下蛋白质组学蛋白质形式鉴定的影响

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-22 DOI: 10.1038/s41592-024-02481-6

Philipp T. Kaulich, Kyowon Jeong, Oliver Kohlbacher, Andreas Tholey

{"title":"Influence of different sample preparation approaches on proteoform identification by top-down proteomics","authors":"Philipp T. Kaulich, Kyowon Jeong, Oliver Kohlbacher, Andreas Tholey","doi":"10.1038/s41592-024-02481-6","DOIUrl":"10.1038/s41592-024-02481-6","url":null,"abstract":"Top-down proteomics using mass spectrometry facilitates the identification of intact proteoforms, that is, all molecular forms of proteins. Multiple past advances have lead to the development of numerous sample preparation workflows. Here we systematically investigated the influence of different sample preparation steps on proteoform and protein identifications, including cell lysis, reduction and alkylation, proteoform enrichment, purification and fractionation. We found that all steps in sample preparation influence the subset of proteoforms identified (for example, their number, confidence, physicochemical properties and artificially generated modifications). The various sample preparation strategies resulted in complementary identifications, substantially increasing the proteome coverage. Overall, we identified 13,975 proteoforms from 2,720 proteins of human Caco-2 cells. The results presented can serve as suggestions for designing and adapting top-down proteomics sample preparation strategies to particular research questions. Moreover, we expect that the sampling bias and modifications identified at the intact protein level will also be useful in improving bottom-up proteomics approaches. A systematic analysis of the influence of different sample preparation steps on proteoform identification by top-down proteomics serves as a useful reference for designing appropriate workflows for specific research questions.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 12","pages":"2397-2407"},"PeriodicalIF":36.1,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02481-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504535","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}

引用次数: 0

Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells 从诱导多能干细胞分化出内脏感觉神经节器官组织。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-22 DOI: 10.1038/s41592-024-02455-8

Kyusik Ahn, Hwee-Seon Park, Sieun Choi, Hojeong Lee, Hyunjung Choi, Seok Beom Hong, Jihui Han, Jong Won Han, Jinchul Ahn, Jaehoon Song, Kyunghyuk Park, Bukyung Cha, Minseop Kim, Hui-Wen Liu, Hyeonggyu Song, Sang Jeong Kim, Seok Chung, Jong-Il Kim, Inhee Mook-Jung

{"title":"Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells","authors":"Kyusik Ahn, Hwee-Seon Park, Sieun Choi, Hojeong Lee, Hyunjung Choi, Seok Beom Hong, Jihui Han, Jong Won Han, Jinchul Ahn, Jaehoon Song, Kyunghyuk Park, Bukyung Cha, Minseop Kim, Hui-Wen Liu, Hyeonggyu Song, Sang Jeong Kim, Seok Chung, Jong-Il Kim, Inhee Mook-Jung","doi":"10.1038/s41592-024-02455-8","DOIUrl":"10.1038/s41592-024-02455-8","url":null,"abstract":"The ability to generate visceral sensory neurons (VSN) from induced pluripotent stem (iPS) cells may help to gain insights into how the gut–nerve–brain axis is involved in neurological disorders. We established a protocol to differentiate human iPS-cell-derived visceral sensory ganglion organoids (VSGOs). VSGOs exhibit canonical VSN markers, and single-cell RNA sequencing revealed heterogenous molecular signatures and developmental trajectories of VSGOs aligned with native VSN. We integrated VSGOs with human colon organoids on a microfluidic device and applied this axis-on-a-chip model to Alzheimer’s disease. Our results suggest that VSN could be a potential mediator for propagating gut-derived amyloid and tau to the brain in an APOE4- and LRP1-dependent manner. Furthermore, our approach was extended to include patient-derived iPS cells, which demonstrated a strong correlation with clinical data. A protocol for differentiating visceral sensory ganglion organoids from induced pluripotent stem cells allows the establishment of an in vitro model for the gut–visceral nerve–brain axis and study of the propagation of pathogenic proteins involved in Alzheimer’s disease along the vagus nerve.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2135-2146"},"PeriodicalIF":36.1,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504533","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}

引用次数: 0

A data portal for providing standardized annotations for cryo-electron tomography 为低温电子断层扫描提供标准化注释的数据门户。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-21 DOI: 10.1038/s41592-024-02477-2

Utz Ermel, Anchi Cheng, Jun Xi Ni, Jessica Gadling, Manasa Venkatakrishnan, Kira Evans, Jeremy Asuncion, Andrew Sweet, Janeece Pourroy, Zun Shi Wang, Kandarp Khandwala, Benjamin Nelson, Dannielle McCarthy, Eric M. Wang, Richa Agarwal, Bridget Carragher

引用次数: 0

Measuring multiple intracellular biochemical properties of proteins with next-generation sequencing 利用新一代测序技术测量蛋白质的多种细胞内生化特性。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-21 DOI: 10.1038/s41592-024-02461-w

引用次数: 0

DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model DiffModeler：利用扩散模型为低温电子显微镜图建立大分子结构模型。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-21 DOI: 10.1038/s41592-024-02479-0

Xiao Wang, Han Zhu, Genki Terashi, Manav Taluja, Daisuke Kihara

引用次数: 0

Constructing and personalizing population pangenome graphs 构建和个性化人口泛基因组图谱。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-21 DOI: 10.1038/s41592-024-02402-7

Rayan Chikhi, Yoann Dufresne, Paul Medvedev

引用次数: 0

Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq 利用 LABEL-seq 对细胞内蛋白质的丰度、活性、相互作用和可药性进行多重分析。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-21 DOI: 10.1038/s41592-024-02456-7

Jessica J. Simon, Douglas M. Fowler, Dustin J. Maly

{"title":"Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq","authors":"Jessica J. Simon, Douglas M. Fowler, Dustin J. Maly","doi":"10.1038/s41592-024-02456-7","DOIUrl":"10.1038/s41592-024-02456-7","url":null,"abstract":"Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein–protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability. Labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq) enables massively parallel profiling of thousands of pooled protein variants in cells, yielding insight into protein function, interactions and druggability.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2094-2106"},"PeriodicalIF":36.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470444","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}

引用次数: 0

Building pangenome graphs 构建泛基因组图谱

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-21 DOI: 10.1038/s41592-024-02430-3

Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G. Ashbrook, Kaisa Thorell, Rachel L. Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Agnieszka A. Golicz, Sven Nahnsen, Zuyu Yang, Moses Njagi Mwaniki, Franklin L. Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H. Sudmant, Sanwen Huang, Detlef Weigel, Nicole Soranzo, Vincenza Colonna, Robert W. Williams, Pjotr Prins

{"title":"Building pangenome graphs","authors":"Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G. Ashbrook, Kaisa Thorell, Rachel L. Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Agnieszka A. Golicz, Sven Nahnsen, Zuyu Yang, Moses Njagi Mwaniki, Franklin L. Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H. Sudmant, Sanwen Huang, Detlef Weigel, Nicole Soranzo, Vincenza Colonna, Robert W. Williams, Pjotr Prins","doi":"10.1038/s41592-024-02430-3","DOIUrl":"10.1038/s41592-024-02430-3","url":null,"abstract":"Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships. PGGB is a modular framework for efficiently building unbiased pangenome graphs, supporting diverse downstream analyses.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2008-2012"},"PeriodicalIF":36.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470437","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}

引用次数: 0

Ultra-high-field MRI for fast imaging of the human brain at mesoscale resolution 超高场磁共振成像技术，用于以中尺度分辨率对人脑进行快速成像。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-17 DOI: 10.1038/s41592-024-02473-6

引用次数: 0

In vivo imaging of the human brain with the Iseult 11.7-T MRI scanner 使用 Iseult 11.7-T 核磁共振成像扫描仪对人脑进行活体成像。

IF 36.1 1区生物学

Nature Methods Pub Date : 2024-10-17 DOI: 10.1038/s41592-024-02472-7

Nicolas Boulant, Franck Mauconduit, Vincent Gras, Alexis Amadon, Caroline Le Ster, Michel Luong, Aurélien Massire, Christophe Pallier, Laure Sabatier, Michel Bottlaender, Alexandre Vignaud, Denis Le Bihan

{"title":"In vivo imaging of the human brain with the Iseult 11.7-T MRI scanner","authors":"Nicolas Boulant, Franck Mauconduit, Vincent Gras, Alexis Amadon, Caroline Le Ster, Michel Luong, Aurélien Massire, Christophe Pallier, Laure Sabatier, Michel Bottlaender, Alexandre Vignaud, Denis Le Bihan","doi":"10.1038/s41592-024-02472-7","DOIUrl":"10.1038/s41592-024-02472-7","url":null,"abstract":"The understanding of the human brain is one of the main scientific challenges of the twenty-first century. In the early 2000s, the French Atomic Energy Commission launched a program to conceive and build a human magnetic resonance imaging scanner operating at 11.7 T. We have now acquired human brain images in vivo at such a magnetic field. We deployed parallel transmission tools to mitigate the radiofrequency field inhomogeneity problem and tame the specific absorption rate. The safety of human imaging at such high field strength was demonstrated using physiological, vestibular, behavioral and genotoxicity measurements on the imaged volunteers. Our technology yields T2 and T2*-weighted images reaching mesoscale resolutions within short acquisition times and with a high signal and contrast-to-noise ratio. In a technological tour de force, a whole-body 11.7-T MRI scanner has been developed. Here images of the human brain are presented while safety for the imaged human volunteers has been ascertained.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2013-2016"},"PeriodicalIF":36.1,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02472-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470441","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}

引用次数: 0