26 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…
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…
Oliver M. Crook, Claire M. Mulvey, Paul D. W. Kirk, Kathryn S. Lilley + 2 more
Analysis of the spatial sub-cellular distribution of proteins is of vital importance to fully understand context specific protein function. Some proteins can be found with a single location within a cell, but up to half of proteins may reside in multiple locations, can dynamically re-localise, or reside within an…
Oliver M. Crook, Claire M. Mulvey, Paul D. W. Kirk, Kathryn S. Lilley + 1 more
Analysis of the spatial sub-cellular distribution of proteins is of vital importance to fully understand context specific protein function. Some proteins can be found with a single location within a cell, but up to half of proteins may reside in multiple locations, can dynamically re-localise, or reside within an…
Lisa M. Breckels, Sean Holden, David Wojnar, Claire M. Mulvey + 6 more
Sub-cellular localisation of proteins is an essential post-translational regulatory mechanism that can be assayed using high-throughput mass spectrometry (MS). These MS-based spatial proteomics experiments enable us to pinpoint the sub-cellular distribution of thousands of proteins in a specific system under controlled…
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…
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…
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 + 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…
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…
Laurent Gatto, Lisa M. Breckels, Kathryn S. Lilley
The sub-cellular localisation of a protein is vital in defining its function, and a protein's mis-localisation is known to lead to adverse effect. As a result, numerous experimental techniques and datasets have been published, with the aim of deciphering the localisation of proteins at various scales and resolutions…
Zhao, Bokai, Shi, Weiyang + 10 more
1 School of Artificial Intelligence, University of Chinese Academy of Sciences. 2 Brainnetome Center, Institute of Automation, Chinese Academy of Sciences. 3 Beijing Key Laboratory of Brainnetome and Brain-Computer Interface, Institute of Automation, Chinese Academy of Sciences, Beijing, China. correspondence author B…
Oliver M. Crook, Kathryn S. Lilley, Laurent Gatto, Paul Kirk
Understanding sub-cellular protein localisation is an essential component to analyse context specific protein function. Recent advances in quantitative massspectrometry (MS) have led to high resolution mapping of thousands of proteins to subcellular locations within the cell. Novel modelling considerations to capture…
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.…
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…
Lyron Winderbaum, Inge Koch, Ove Gustafsson, Stephan Meding + 1 more
'Peter Hoffmann'] Imaging mass spectrometry (IMS) has transformed proteomics by providing an avenue for collecting spatially distributed molecular data. Mass spectrometry data acquired with matrix assisted laser desorption ionization (MALDI) IMS consist of tens of thousands of spectra, measured at regular grid points…
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…
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”…
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…
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…
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
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…
Authors not listed
Photo-affinity labeling (PAL) utilizes photoreactive molecules to derivatize proteins in a solvent-accessible depend-ent manner. The site and frequency of the products of this reaction can be used to garner insights into the confor-mation of the protein. In this work, we document and characterize a novel oxidation…
Authors not listed
Fragment based drug design (FBDD) is like a chess game in that a good or a bad move can dramatically influence the outcome. At the start of the design process, it is important to identify the key binding site residues (hotspots) that can have a substantial impact on ligand efficiency (LE) and binding. Here, we…