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Spatial proteomics of vesicular trafficking: coupling mass spectrometry and imaging approaches in membrane biology

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Preparative free‐flow electrophoresis, a versatile technology complementing gradient centrifugation in the isolation of highly purified cell organelles

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Integrative Chemical Proteomics and Cell Biology Methods to Study Endocytosis and Vesicular Trafficking in Arabidopsis

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In Vivo Identification of Plant Protein Complexes Using IP-MS/MS

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Light Sheet Fluorescence Microscopy Optimized for Long-Term Imaging of Arabidopsis Root Development

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Using FM Dyes to Study Endomembranes and Their Dynamics in Plants and Cell Suspensions

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Separation of the Plant Golgi Apparatus and Endoplasmic Reticulum by Free-Flow Electrophoresis

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Split-luciferase complementary assay: applications, recent developments, and future perspectives

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FRET-FLIM applications in plant systems

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Fluid-phase and membrane markers reveal spatio-temporal dynamics of membrane traffic and repair in the green alga Chara australis

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Techniques for detecting protein-protein interactions in living cells: principles, limitations, and recent progress

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The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants

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An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells

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Multicolor 3D-dSTORM Reveals Native-State Ultrastructure of Polysaccharides' Network during Plant Cell Wall Assembly

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The dynamics and endocytosis of Flot1 protein in response to flg22 in Arabidopsis

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Gel electrophoresis-based plant proteomics: Past, present, and future. Happy 10th anniversary Journal of Proteomics!

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SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

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Spatiotemporal Dynamics of the BRI1 Receptor and its Regulation by Membrane Microdomains in Living Arabidopsis Cells

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Arabidopsis Synaptotagmin 2 Participates in Pollen Germination and Tube Growth and Is Delivered to Plasma Membrane via Conventional Secretion

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Quantification of Membrane Protein Dynamics and Interactions in Plant Cells by Fluorescence Correlation Spectroscopy

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Membrane Trafficking in Plant Immunity

inferredcites →https://doi.org/10.1016/j.molp.2018.04.003openalex-snapshot

Arabidopsis Blue Light Receptor Phototropin 1 Undergoes Blue Light-Induced Activation in Membrane Microdomains

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Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression

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Vesicle trafficking in plant immunity

inferredcites →https://doi.org/10.1016/j.plantsci.2018.04.008openalex-snapshot

Knowns and unknowns of plasma membrane protein degradation in plants

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High-Content Screening for Quantitative Cell Biology

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Vacuole Biogenesis in Plants: How Many Vacuoles, How Many Models?

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Mass Spectrometry Untangles Plant Membrane Protein Signaling Networks

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Organellar Proteomic Profiling to Analyze Membrane Trafficking Pathways

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Proximity labeling: an emerging tool for probing in planta molecular interactions

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Split-HaloTag imaging assay for sophisticated microscopy of protein–protein interactions in planta

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TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set

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Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings

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Proteomics on Brefeldin A-Treated Arabidopsis Roots Reveals Profilin 2 as a New Protein Involved in the Cross-Talk between Vesicular Trafficking and the Actin Cytoskeleton

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Wortmannin Treatment Induces Changes in Arabidopsis Root Proteome and Post-Golgi Compartments

inferredcites →https://doi.org/10.1021/pr4008464openalex-snapshot

Identification of Trans-Golgi Network Proteins in Arabidopsis thaliana Root Tissue

inferredcites →https://doi.org/10.1038/cr.2011.129openalex-snapshot

Isolation and proteomic analysis of the SYP61 compartment reveal its role in exocytic trafficking in Arabidopsis

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Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy

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Efficient proximity labeling in living cells and organisms with TurboID

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Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ

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Correlated light and electron microscopy: ultrastructure lights up!

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An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

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Preparation of plants for developmental and cellular imaging by light-sheet microscopy

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Superresolution live imaging of plant cells using structured illumination microscopy

inferredcites →https://doi.org/10.1038/nprot.2015.100openalex-snapshot

Imaging fluorescence (cross-) correlation spectroscopy in live cells and organisms

inferredcites →https://doi.org/10.1038/nprot.2017.026openalex-snapshot

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome

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Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics

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Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

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TurboID-based proximity labeling reveals that UBR7 is a regulator of N NLR immune receptor-mediated immunity

inferredcites →https://doi.org/10.1038/s41467-020-19840-4openalex-snapshot

Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers

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Cargo sorting zones in the trans-Golgi network visualized by super-resolution confocal live imaging microscopy in plants

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Multiscale imaging of plant development by light-sheet fluorescence microscopy

inferredcites →https://doi.org/10.1038/s41477-018-0328-1openalex-snapshot

A whole-cell electron tomography model of vacuole biogenesis in Arabidopsis root cells

inferredcites →https://doi.org/10.1038/s41477-019-0365-4openalex-snapshot

Arbuscular cell invasion coincides with extracellular vesicles and membrane tubules

inferredcites →https://doi.org/10.1038/s41477-021-00997-9openalex-snapshot

A distinct giant coat protein complex II vesicle population in Arabidopsis thaliana

inferredcites →https://doi.org/10.1038/s41556-021-00693-yopenalex-snapshot

Quantitative proteomics identifies the core proteome of exosomes with syntenin-1 as the highest abundant protein and a putative universal biomarker

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Proteomic and interactomic insights into the molecular basis of cell functional diversity

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Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy

inferredcites →https://doi.org/10.1038/s41592-018-0005-3openalex-snapshot

Self-interference 3D super-resolution microscopy for deep tissue investigations

inferredcites →https://doi.org/10.1038/s41592-020-01010-5openalex-snapshot

Deciphering molecular interactions by proximity labeling

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Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

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Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues

inferredcites →https://doi.org/10.1038/s41598-018-27500-3openalex-snapshot

In planta proximity dependent biotin identification (BioID)

inferredcites →https://doi.org/10.1038/s43586-021-00029-yopenalex-snapshot

Subcellular proteomics

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Photosystem II antenna phosphorylation-dependent protein diffusion determined by fluorescence correlation spectroscopy

inferredcites →https://doi.org/10.1038/srep19419openalex-snapshot

Two-Photon Excitation STED Microscopy with Time-Gated Detection

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Studying protein–protein interactions: progress, pitfalls and solutions

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Probing nuclear pore complex architecture with proximity-dependent biotinylation

inferredcites →https://doi.org/10.1073/pnas.1517445113openalex-snapshot

Actin-dependent vacuolar occupancy of the cell determines auxin-induced growth repression

inferredcites →https://doi.org/10.1073/pnas.1616299114openalex-snapshot

ATG9 regulates autophagosome progression from the endoplasmic reticulum in Arabidopsis

inferredcites →https://doi.org/10.1073/pnas.1717839115openalex-snapshot

Distinct sets of tethering complexes, SNARE complexes, and Rab GTPases mediate membrane fusion at the vacuole in Arabidopsis

inferredcites →https://doi.org/10.1073/pnas.2011152117openalex-snapshot

Longin R-SNARE is retrieved from the plasma membrane by ANTH domain-containing proteins in Arabidopsis

inferredcites →https://doi.org/10.1074/jbc.m110.160531openalex-snapshot

PAMP (Pathogen-associated Molecular Pattern)-induced Changes in Plasma Membrane Compartmentalization Reveal Novel Components of Plant Immunity

inferredcites →https://doi.org/10.1074/jbc.m406644200openalex-snapshot

Proteomics of Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC) Membranes from Brefeldin A-treated HepG2 Cells Identifies ERGIC-32, a New Cycling Protein That Interacts with Human Erv46

inferredcites →https://doi.org/10.1074/mcp.m115.050286openalex-snapshot

Identification of Regulatory and Cargo Proteins of Endosomal and Secretory Pathways in Arabidopsis thaliana by Proteomic Dissection*

inferredcites →https://doi.org/10.1074/mcp.m116.060129openalex-snapshot

Identification of Cargo for Adaptor Protein (AP) Complexes 3 and 4 by Sucrose Gradient Profiling

inferredcites →https://doi.org/10.1074/mcp.m700566-mcp200openalex-snapshot

Multiple Phosphorylations in the C-terminal Tail of Plant Plasma Membrane Aquaporins

inferredcites →https://doi.org/10.1074/mcp.m900090-mcp200openalex-snapshot

Quantitative Proteomics Reveals a Dynamic Association of Proteins to Detergent-resistant Membranes upon Elicitor Signaling in Tobacco

inferredcites →https://doi.org/10.1074/mcp.ra119.001336openalex-snapshot

Sucrose-induced Receptor Kinase 1 is Modulated by an Interacting Kinase with Short Extracellular Domain*

inferredcites →https://doi.org/10.1074/mcp.t400009-mcp200openalex-snapshot

Localization of Organelle Proteins by Isotope Tagging (LOPIT)

inferredcites →https://doi.org/10.1083/jcb.201111049openalex-snapshot

Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles

inferredcites →https://doi.org/10.1091/mbc.e16-03-0164openalex-snapshot

Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy

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Electron tomography in plant cell biology

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Merging roads: chemical tools and cell biology to study unconventional protein secretion

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Interactomics of Qa-SNARE in Arabidopsis thaliana

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Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process

inferredcites →https://doi.org/10.1093/plcell/koab116openalex-snapshot

Arabidopsis myosin XIK interacts with the exocyst complex to facilitate vesicle tethering during exocytosis

inferredcites →https://doi.org/10.1093/plcell/koab235openalex-snapshot

Molecular mechanisms of endomembrane trafficking in plants

inferredcites →https://doi.org/10.1093/plcell/koab237openalex-snapshot

Imaging the living plant cell: From probes to quantification

inferredcites →https://doi.org/10.1093/plcell/koac071openalex-snapshot

Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components

inferredcites →https://doi.org/10.1093/plphys/kiaa040openalex-snapshot

Membrane imaging in the plant endomembrane system

inferredcites →https://doi.org/10.1093/plphys/kiab349openalex-snapshot

Imaging plant cells and organs with light-sheet and super-resolution microscopy

inferredcites →https://doi.org/10.1093/plphys/kiac123openalex-snapshot

Salt stress alters membrane lipid content and lipid biosynthesis pathways in the plasma membrane and tonoplast

inferredcites →https://doi.org/10.1093/plphys/kiac167openalex-snapshot

Arabidopsis HOPS subunit VPS41 carries out plant-specific roles in vacuolar transport and vegetative growth

inferredcites →https://doi.org/10.1104/pp.112.204263openalex-snapshot

Putative Glycosyltransferases and Other Plant Golgi Apparatus Proteins Are Revealed by LOPIT Proteomics

inferredcites →https://doi.org/10.1104/pp.114.235804openalex-snapshot

The Plant Membrane-Associated REMORIN1.3 Accumulates in Discrete Perihaustorial Domains and Enhances Susceptibility to Phytophthora infestans

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Label-Free Protein Quantification for Plant Golgi Protein Localization and Abundance

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Putting the Squeeze on Plasmodesmata: A Role for Reticulons in Primary Plasmodesmata Formation

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Advances in Imaging Plant Cell Dynamics

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Protein Storage Vacuoles Originate from Remodeled Preexisting Vacuoles in Arabidopsis thaliana

inferredcites →https://doi.org/10.1104/pp.18.00832openalex-snapshot

SNAREs SYP121 and SYP122 Mediate the Secretion of Distinct Cargo Subsets

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Osmotic Stress Activates Two Reactive Oxygen Species Pathways with Distinct Effects on Protein Nanodomains and Diffusion

inferredcites →https://doi.org/10.1104/pp.18.01228openalex-snapshot

A Golgi-Released Subpopulation of the Trans-Golgi Network Mediates Protein Secretion in Arabidopsis

inferredcites →https://doi.org/10.1105/tpc.113.122358openalex-snapshot

Clathrin and Membrane Microdomains Cooperatively Regulate RbohD Dynamics and Activity in Arabidopsis

inferredcites →https://doi.org/10.1105/tpc.15.00154openalex-snapshot

Salt-Induced Remodeling of Spatially Restricted Clathrin-Independent Endocytic Pathways in Arabidopsis Root

inferredcites →https://doi.org/10.1105/tpc.17.00785openalex-snapshot

A Functional Study of AUXILIN-LIKE1 and 2, Two Putative Clathrin Uncoating Factors in Arabidopsis

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Glycome and Proteome Components of Golgi Membranes Are Common between Two Angiosperms with Distinct Cell-Wall Structures

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A Hybrid Approach Enabling Large-Scale Glycomic Analysis of Post-Golgi Vesicles Reveals a Transport Route for Polysaccharides

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Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization

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AtTRAPPC11/ROG2: A Role for TRAPPs in Maintenance of the Plant Trans-Golgi Network/Early Endosome Organization and Function

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Secretion of Phospholipase Dδ Functions as a Regulatory Mechanism in Plant Innate Immunity

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Multiple Quality Control Mechanisms in the ER and TGN Determine Subcellular Dynamics and Salt-Stress Tolerance Function of KORRIGAN1

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Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems

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Covalent Self-Labeling of Tagged Proteins with Chemical Fluorescent Dyes in BY-2 Cells and Arabidopsis Seedlings

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Volume scanning electron microscopy for imaging biological ultrastructure

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Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set

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Comparative analysis of phytohormone-responsive phosphoproteins in Arabidopsis thaliana using TiO2-phosphopeptide enrichment and mass accuracy precursor alignment

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SYP22 and VAMP727 regulate BRI1 plasma membrane targeting to control plant growth in Arabidopsis

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At the intersection of exocytosis and endocytosis in plants

inferredcites →https://doi.org/10.1111/nph.17017openalex-snapshot

Plasma membrane calcineurin B‐like calcium‐ion sensor proteins function in regulating primary root growth and nitrate uptake by affecting global phosphorylation patterns and microdomain protein distribution

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A distinct class of vesicles derived from thetrans‐Golgi mediates secretion of xylogalacturonan in the root border cell

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Rapid and reproducible phosphopeptide enrichment by tandem metal oxide affinity chromatography : application to boron deficiency induced phosphoproteomics

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SNARE proteins VAMP721 and VAMP722 mediate the post‐Golgi trafficking required for auxin‐mediated development in Arabidopsis

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Measuring Exocytosis Rate Using Corrected Fluorescence Recovery After Photoconversion

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Developmental control of plant Rho GTPase nano-organization by the lipid phosphatidylserine

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The GATOR–Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids

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Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells

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Multicolour three dimensional structured illumination microscopy of immunolabeled plant microtubules and associated proteins

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Dynamic analysis of Arabidopsis AP2 σ subunit reveals a key role in clathrin-mediated endocytosis and plant development

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Sterols regulate endocytic pathways during flg22-induced defense responses in Arabidopsis

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The Golgi entry core compartment functions as a COPII-independent scaffold for ER-to-Golgi transport in plant cells

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A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

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Proteomic Profiling of Autophagosome Cargo in Saccharomyces cerevisiae

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Interaction of the Trans-Frame Potyvirus Protein P3N-PIPO with Host Protein PCaP1 Facilitates Potyvirus Movement

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A Flow Cytometry-Based Phenotypic Screen To Identify Novel Endocytic Factors inSaccharomyces cerevisiae

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Bimolecular Fluorescence Complementation (BiFC): A 5-year Update and Future Perspectives

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A novel orange-colored bimolecular fluorescence complementation (BiFC) assay using monomeric Kusabira-Orange protein

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Endosomal Interactions during Root Hair Growth

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Super-resolution Microscopy – Applications in Plant Cell Research

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Alfalfa Root Growth Rate Correlates with Progression of Microtubules during Mitosis and Cytokinesis as Revealed by Environmental Light-Sheet Microscopy

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Understanding FRET as a Research Tool for Cellular Studies

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Membrane Profiling by Free Flow Electrophoresis and SWATH-MS to Characterize Subcellular Compartment Proteomes in Mesembryanthemum crystallinum

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Fluorescent Nano-Probes to Image Plant Cell Walls by Super-Resolution STED Microscopy

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Global, quantitative and dynamic mapping of protein subcellular localization

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Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation

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Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

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Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID

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Localization, proteomics, and metabolite profiling reveal a putative vesicular transporter for UDP-glucose

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Decoding plant complexity through spatially resolved multi-omics approaches

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Genetically encoded biosensors for spatiotemporal monitoring of plant proteins in growth and stress responses

inferred← citeshttps://doi.org/10.1016/j.biosx.2026.100768openalex-snapshot

Sensing plant stress: Biosensor technologies for abscisic acid monitoring

inferred← citeshttps://doi.org/10.1016/j.cj.2023.05.014openalex-snapshot

Reversible protein phosphorylation, a central signaling hub to regulate carbohydrate metabolic networks

inferred← citeshttps://doi.org/10.1016/j.egg.2026.100454openalex-snapshot

Crop production under abiotic stresses: Management options and crop reactions

inferred← citeshttps://doi.org/10.1016/j.heliyon.2023.e21976openalex-snapshot

RETRACTED: Synergism of vesicle trafficking and cytoskeleton during regulation of plant growth and development: A mechanistic outlook

inferred← citeshttps://doi.org/10.1016/j.pbi.2025.102708openalex-snapshot

Current insights into plant volatile organic compound biosynthesis

inferred← citeshttps://doi.org/10.1016/j.stress.2026.101353openalex-snapshot

Novel approaches to functional studies of stress-related proteins in wheat and barley: Genetic engineering, proteoforms, organellar proteomics, interactomics and proxiomics

inferred← citeshttps://doi.org/10.1016/j.tibtech.2023.05.010openalex-snapshot

Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants

inferred← citeshttps://doi.org/10.1016/j.tplants.2024.05.009openalex-snapshot

Capturing the phosphorylation-linked protein-complex landscape in plants

inferred← citeshttps://doi.org/10.1021/acs.jafc.6c05128openalex-snapshot

Proteomic Evidence Indicates Ultrasound-Assisted Extraction Enhances Recovery of Membrane-Associated Proteins in Hericium erinaceus

inferred← citeshttps://doi.org/10.1039/d3sc03725hopenalex-snapshot

Metal organic layers enabled cell surface engineering coupling biomembrane fusion for dynamic membrane proteome profiling

inferred← citeshttps://doi.org/10.1079/9781836994572.0002openalex-snapshot

Spatial Omics in Plants: Current Achievements, Challenges, and Future Directions

inferred← citeshttps://doi.org/10.1093/bib/bbaf154openalex-snapshot

Integrating CORUM and co-fractionation mass spectrometry to create enhanced benchmarks for protein complex predictions

inferred← citeshttps://doi.org/10.1093/bib/bbag169openalex-snapshot

The good, the bad, and the ugly: opportunities, challenges, and pitfalls in spatial proteomics modeling

inferred← citeshttps://doi.org/10.1093/jxb/erae172openalex-snapshot

More than meets the eye: knowns and unknowns of the trafficking of small secreted proteins in Arabidopsis

inferred← citeshttps://doi.org/10.1094/mpmi-10-23-0167-fiopenalex-snapshot

Unveiling the Slippery Secrets of Saliva: Effector Proteins of Phloem-Feeding Insects

inferred← citeshttps://doi.org/10.20944/preprints202305.1293.v1openalex-snapshot

Recent Developments in High Spatio-Temporal Image-Based Tracking of Proteins in Subcellular Spatial Proteomics Applications

inferred← citeshttps://doi.org/10.21037/jtd-24-1366openalex-snapshot

CLCA1 and BPIFB1 are potential novel biomarkers for asthma: an iTRAQ analysis

inferred← citeshttps://doi.org/10.3389/fnmol.2023.1097633openalex-snapshot

The function of Golgi apparatus in LRRK2-associated Parkinson’s disease

inferred← citeshttps://doi.org/10.3390/cells12151972openalex-snapshot

The Golgi Apparatus: A Voyage through Time, Structure, Function and Implication in Neurodegenerative Disorders

inferred← citeshttps://doi.org/10.3390/su16177651openalex-snapshot

Integrative Approaches to Abiotic Stress Management in Crops: Combining Bioinformatics Educational Tools and Artificial Intelligence Applications

inferred← citeshttps://doi.org/10.4236/jbm.2026.149026openalex-snapshot

Arabidopsis thaliana Type One Protein Phosphatases: Context-Dependent Regulators of Development, Stress Responses, and Immunity

inferred← citeshttps://doi.org/10.7554/elife.96892openalex-snapshot

Untargeted pixel-by-pixel metabolite ratio imaging as a novel tool for biomedical discovery in mass spectrometry imaging

inferred← citeshttps://doi.org/10.7554/elife.96892.1openalex-snapshot

Untargeted Pixel-by-Pixel Imaging of Metabolite Ratio Pairs as a Novel Tool for Biomedical Discovery in Mass Spectrometry Imaging

inferred← citeshttps://doi.org/10.7554/elife.96892.2openalex-snapshot

Untargeted Pixel-by-Pixel Imaging of Metabolite Ratio Pairs as a Novel Tool for Biomedical Discovery in Mass Spectrometry Imaging

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.