23 papers · ranked by Valyu relevance
Peter Horvath, Fabian Coscia
Spatial proteomics offers unprecedented insights into the localization, quantity, and interactions of proteins within cells and tissues, thereby enabling researchers and clinicians to map protein networks with high precision. This powerful approach is currently revolutionizing our understanding of cellular organization…
Yiwen Li, Yusheng Zhang, Ying Zhang, Qing Wang + 3 more
Protein function is inherently spatial: the same molecule can elicit distinct biological outcomes depending on its localization, interacting partners, and surrounding microenvironment. Spatial proteomics enables systematic in situ characterization of protein localization, abundance, and interactions across subcellular…
Yuanwei Xu, T. Mamie Lih, Angelo M. De Marzo, Qing Kay Li + 1 more
Background Spatial proteomics seeks to understand the spatial organization of proteins in tissues or at different subcellular localization in their native environment. However, capturing the spatial organization of proteins is challenging. Here, we present an innovative approach termed Spatial Proteomics through…
Yuanwei Xu, Hyeon-Cheol Park, Jason Li, Yuehan Liu + 4 more
Spatial proteomics aims to characterize proteome in situ with regional resolution, linking molecular states to tissue architecture and microenvironments. While recent advances have expanded our access to spatially resolved proteomics, major barriers in scalability and throughput remain. Building on our prior SPOT…
Ying Jiang, Jian Wang, Aihua Sun, Hongxing Zhang + 18 more
'Weijie Qin' 'Wantao Ying' 'Yanchang Li' 'Cheng Chang' 'Xiaowen Wang' 'Linhai Xie' 'Wei Liu' 'Jialin Liu' 'Xiaomei Zhang' 'Qunjiao Yan' 'Yu Zou' 'Chuanping Zhao' 'Haofan Sun' 'Jian Zhang' 'Shicheng Su' 'Qiang Gao' 'Fuchu He'] Title: ABSTRACT The concept of ‘proteomics-driven precision medicine’ highlighted in 2019…
Yi-Chien Wu, Dylan Schwartz, Elie Abi Khalil, Aditi Upadhye + 2 more
Spatial proteomics uncovers the molecular basis of cellular function in intact tissues. Laser capture microdissection coupled with mass spectrometry enables comprehensive proteomic profiling of selected tissue regions but typically does not support cell-type-specific proteomic analysis. We present NicheProt, a 3D…
Yumi Kwon, Jongmin Woo, Fengchao Yu, Sarah M. Williams + 9 more
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has…
Yumi Kwon, Jongmin Woo, Fengchao Yu, Sarah M. Williams + 9 more
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has…
Ching-Chia Yang, Ching-Ya Lin, Hsin-Yo Yuan, Hsuan-Cheng Huang + 1 more
Mass spectrometry-based spatial omics is a powerful approach for visualizing the spatial organization of proteins, metabolites, lipids, and other biomolecules in situ, combining the molecular depth of mass spectrometry with spatially resolved imaging. This systematic review traces the rapid technological and…
Kristin Burnum-Johnson, Thomas P. Conrads, Richard R. Drake, Amy E. Herr + 16 more
'Amy E. Herr' 'Ravi Iyengar' 'Ryan Kelly' 'Emma Lundberg' 'Michael J. MacCoss' 'Alexandra Naba' 'Garry P. Nolan' 'Pavel A. Pevzner' 'Karin Rodland' 'Salvatore Sechi' 'Nikolai Slavov' 'Jeffrey M. Spraggins' 'Jennifer E. Van Eyk' 'Marc Vidal' 'Christine Vogel' 'David R. Walt' 'Neil L. Kelleher'] Kristin E.…
Yi-De Chen, Chih-Wei Chang, Chantal Hoi Yin Cheung, Hsiao-Jen Chang + 10 more
Microscopy-guided proteomics at an organelle-dimension resolution is desired for revealing unknown protein constituents at specific disease- or functional-associated regions at the molecular-molecular interactions level. Here, we achieve protein spatial purification by introducing a firmware-integrated microscopy…
Stephen Coleman, Lisa Breckels, Ross F. Waller, Kathryn S. Lilley + 3 more
The subcellular localisation of proteins is a key determinant of their function. High-throughput analyses of these localisations can be performed using mass spectrometry-based spatial proteomics, which enables us to examine the localisation and relocalisation of proteins. Furthermore, complementary data sources can…
Liza Löf, Bo Xu, Tanay Kumar Sinha, Caroline Dahlström + 11 more
Improved methods are needed to gain insights in how proteins exert their myriad roles in cells and organs. Multiplex in situ proximity ligation assay (misPLA), described herein, can provide a window into the functional states of proteins in cells and tissues by applying pairs of antibody–oligonucleotide conjugates to…
Stephen Coleman, Lisa Breckels, Ross F. Waller, Kathryn S. Lilley + 4 more
The subcellular localisation of proteins is a key determinant of their function. High-throughput analyses of these localisations can be performed using mass spectrometry-based spatial proteomics, which enables us to examine the localisation and relocalisation of proteins. Furthermore, complementary data sources can…
José Camacho, Michael Armstrong, Luz García, Caridad Díaz + 1 more
'Carolina Gómez‐Llorente'] Over the past few years, technological advances have allowed for measurement of omics data at the cell level, creating a new type of data generally referred to as single-cell (sc) omics. On the other hand, the so-called spatial omics are a family of techniques that generate biological…
Zheng, Ziyue, Jabre, Loay J. + 6 more
Intracellular compartmentalization of proteins underpins their function and the metabolic processes they sustain. Various mass spectrometry–based proteomics methods (subcellular spatial proteomics) now allow high throughput subcellular protein localization. Yet, the curation, analysis and interpretation of these data…
Bryon Drown, Kevin Jooß, Rafael Melani, Cameron Lloyd-Jones + 2 more
A functional understanding of the human body requires structure-function studies of proteins at scale. The chemical structure of proteins is controlled at the transcriptional, translational, and post-translational levels, creating a variety of products with modulated functions within the cell. The term “proteoform”…
Afsaneh Taheri Kal-Koshvandi
We present the first light-free, genetically minimal platform for spatiotemporally resolved proximity labeling across five neuronal compartments—synaptic, nuclear, endosomal, mitochondrial, and activity-dependent microdomains. A covalent "catalyst–luciferase sandwich" architecture site-specifically conjugates five…
Authors not listed
The Golgi apparatus (GA) orchestrates protein modification, trafficking, and secretion through highly dynamic remodeling, yet its proteomic complexity remains difficult to resolve in living systems. Here, we report CAT-Golgi, a genetically independent and light-controlled photocatalytic proximity labeling strategy for…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…
Authors not listed
The analysis of macromolecules - such as proteins - pose a significant bottleneck in analytical science. We have developed surface treatment techniques utilising direct and radiofrequency current argon plasmas, able to quickly digest condensed-phase macromolecules while maintaining spatial resolution of analytes. We…
Yuming Jiang, Rex Devasahayam Arokia Balaya, Dina Schuster, Benjamin A. Neely + 15 more
'Benjamin A. Neely' 'Germán L. Rosano' 'Norbert Volkmar' 'Amanda Momenzadeh' 'Trenton M. Peters-Clarke' 'Susan Egbert' 'Simion Kreimer' 'Emma H. Doud' 'Oliver M. Crook' 'Amit Kumar Yadav' 'Muralidharan Vanuopadath' 'Martín L. Mayta' 'Anna G. Duboff' 'Nicholas M. Riley' 'Robert L. Moritz' 'Jesse G. Meyer'] Proteomics is…
Authors not listed
Plasma proteomics has regained attention in recent years through advancements in mass spectrometry instrumentation and sample preparation, as well as new high-throughput affinity-based technologies. Here, we evaluate the analytical performance of the new Olink Reveal platform, a proximity extension assay (PEA)-based…