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N-Glyco & Plasma membrane Proteomics in Plants
focus on plant-pathogen interactions and plant physiology
Curated by Song Wei
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N-glycan occupancy of Arabidopsis N-glycoproteins

N-glycan occupancy of Arabidopsis N-glycoproteins | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
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A workflow for large-scale empirical identification of cell wall N-linked glycoproteins of tomato (Solanum lycopersicum) fruit by tandem mass spectrometry - Thannhauser - ELECTROPHORESIS - Wiley On...

A workflow for large-scale empirical identification of cell wall N-linked glycoproteins of tomato (Solanum lycopersicum) fruit by tandem mass spectrometry - Thannhauser - ELECTROPHORESIS - Wiley On... | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
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ScienceDirect.com - Molecular Cell - Mapping N-Glycosylation Sites across Seven Evolutionarily Distant Species Reveals a Divergent Substrate Proteome Despite a Common Core Machinery

ScienceDirect.com - Molecular Cell - Mapping N-Glycosylation Sites across Seven Evolutionarily Distant Species Reveals a Divergent Substrate Proteome Despite a Common Core Machinery | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
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Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling

Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
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Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures - Li - 2009 - PROTEOMICS - Wiley Online ...

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Chemical Deamidation: A Common Pitfall in Large-Scale N-Linked Glycoproteomic Mass Spectrometry-Based Analyses - Journal of Proteome Research (ACS Publications)

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GABI Primary Database ( GabiPD ) - Genomanalyse im biologischen System Pflanze

GabiPD (Genomanalyse im biologischen System Pflanze) Primary Database:
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MapMan

MapMan | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes.
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DAVID Functional Annotation Bioinformatics Microarray Analysis

DAVID Functional Annotation Bioinformatics Microarray Analysis | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
You can use SMART in two different modes: normal or genomic.The main difference is in the underlying protein database used. In Normal SMART, the database contains Swiss-Prot, SP-TrEMBL and stable Ensembl proteomes. In Genomic SMART, only the proteomes of completely sequenced genomes are used; Ensembl for metazoans and Swiss-Prot for the rest. The complete list of genomes in Genomic SMART is available here.
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The Secreted Plant N-Glycoproteome and Associated Secretory Pathways

The Secreted Plant N-Glycoproteome and Associated Secretory Pathways | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it

N-Glycosylation is a common form of eukaryotic protein post-translational modification, and one that is particularly prevalent in plant cell wall proteins. Large scale and detailed characterization of N-glycoproteins therefore has considerable potential in better understanding the composition and functions of the cell wall proteome, as well as those proteins that reside in other compartments of the secretory pathway. While there have been numerous studies of mammalian and yeast N-glycoproteins, less is known about the population complexity, biosynthesis, structural variation, and trafficking of their plant counterparts. However, technical developments in the analysis of glycoproteins and the structures the glycans that they bear, as well as valuable comparative analyses with non-plant systems, are providing new insights into features that are common among eukaryotes and those that are specific to plants, some of which may reflect the unique nature of the plant cell wall. In this review we present an overview of the current knowledge of plant N-glycoprotein synthesis and trafficking, with particular reference to those that are cell wall localized.

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Cell Host & Microbe - Phytopathogen Effectors Subverting Host Immunity: Different Foes, Similar Battleground

Cell Host & Microbe - Phytopathogen Effectors Subverting Host Immunity: Different Foes, Similar Battleground | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it

Phytopathogenic bacteria, fungi, and oomycetes invade and colonize their host plants through distinct routes. These pathogens secrete diverse groups of effector proteins that aid infection and establishment of different parasitic lifestyles. Despite this diversity, a comparison of different plant-pathogen systems has revealed remarkable similarities in the host immune pathways targeted by effectors from distinct pathogen groups. Immune signaling pathways mediated by pattern recognition receptors, phytohormone homeostasis or signaling, defenses associated with host secretory pathways and pathogen penetrations, and plant cell death represent some of the key processes controlling disease resistance against diverse pathogens. These immune pathways are targeted by effectors that carry a wide range of biochemical functions and are secreted by completely different pathogen groups, suggesting that these pathways are a common battleground encountered by many plant pathogens.

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Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling

The plant plasma membrane is a crucial mediator of the interaction between plants and microbes. Understanding how the plasma membrane proteome responds to diverse immune signaling events will lead to a greater understanding of plant immunity and uncover novel targets for crop improvement. Here we report the results from a large scale quantitative proteomics study of plasma membrane-enriched fractions upon activation of the Arabidopsis thaliana immune receptor RPS2. More than 2300 proteins were identified in total, with 1353 proteins reproducibly identified across multiple replications. Label-free spectral counting was employed to quantify the relative protein abundance between different treatment samples. Over 20% of up-regulated proteins have known roles in plant immune responses. Significantly changing proteins include those involved in calcium and lipid signaling, membrane transport, primary and secondary metabolism, protein phosphorylation, redox homeostasis, and vesicle trafficking. A subset of differentially regulated proteins was independently validated during bacterial infection. This study presents the largest quantitative proteomics data set of plant immunity to date and provides a framework for understanding global plasma membrane proteome dynamics during plant immune responses.

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N-Linked Global Glycan Profiling by NanoLC Mass Spectrometry - Springer

N-Linked Global Glycan Profiling by NanoLC Mass Spectrometry - Springer | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it

A method is detailed for the global profiling of underivatized N-linked glycans that are derived from complex protein mixtures. The method consists of five main steps that include the following: (1) protein denaturation; (2) enzymatic digestion; (3) solid phase extraction; (4) nanoLC MS analysis; and (5) data interpretation. Materials, methods, and algorithms for the identification of both glycan composition and structure are summarized. In addition, potential problems and their resolutions are addressed.

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Advances in purification and separation of posttranslationally modified proteins

Advances in purification and separation of posttranslationally modified proteins | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
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ScienceDirect.com - Cell - Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints

ScienceDirect.com - Cell - Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
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Glycocapture-based proteomics for secretome analysis - Lai - 2013 - PROTEOMICS - Wiley Online Library

Glycocapture-based proteomics for secretome analysis - Lai - 2013 - PROTEOMICS - Wiley Online Library | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
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The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS - Geromanos - 2009 - PROTEOMICS - Wiley Online Library

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Frontiers | Plant secretome proteomics | Frontiers in Plant Proteomics

Frontiers | Plant secretome proteomics | Frontiers in Plant Proteomics | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
The plant secretome refers to the set of proteins secreted out of the plant cell into the surrounding extra-cellular space commonly referred to as the apoplast.
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Galaxy/NBIC tools

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Protein Identifier Cross-Reference Service

Protein Identifier Cross-Reference Service | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
The Protein Identifier Mapping Service provides a free interface to resolve
protein identifiers across multiple databases that correspond to the same
logical protein.
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SMART: Main page

SMART: Main page | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it
You can use SMART in two different modes: normal or genomic.The main difference is in the underlying protein database used. In Normal SMART, the database contains Swiss-Prot, SP-TrEMBL and stable Ensembl proteomes. In Genomic SMART, only the proteomes of completely sequenced genomes are used; Ensembl for metazoans and Swiss-Prot for the rest. The complete list of genomes in Genomic SMART is available here.
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Analytical technologies for identification and characterization of the plant N-glycoproteome

N-glycosylation is one of the most common and complex post-translational modifications of eukaryotic proteins and one that has numerous roles, such as modulating protein stability, sorting, folding, enzyme activity, and ligand interactions. In plants, the functional significance of N-glycosylation is typically obscure, although it is a feature of most secreted proteins and so is potentially of considerable interest to plant cell wall biologists. While analytical pipelines have been established to characterize yeast, mammalian, and bacterial N-glycoproteomes, such large-scale approaches for the study of plant glycoproteins have yet to be reported. Indeed, the N-glycans that decorate plant and mammalian or yeast proteins are structurally distinct and so modification of existing analytical approaches are needed to tackle plant N-glycoproteomes. In this review, we summarize a range of existing technologies for large-scale N-glycoprotein analysis and highlight promising future approaches that may provide a better understanding of the plant N-glycoproteome, and therefore the cell wall proteome and other proteins associated with the secretory pathway.

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Current Opinion in Chemical Biology - Glycomics, glycoproteomics and the immune system

Current Opinion in Chemical Biology - Glycomics, glycoproteomics and the immune system | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it

Glycomics and glycoproteomics have become indispensible tools in the study of glycoconjugates. Mass spectrometry based methods are standardly used to study the proteome and/or glycome and these approaches are capable of providing both, qualitative and quantitative information using top down techniques. The human immune system marks a particular area of interest for glycomics and glycoproteomics research since a large number of key proteins in innate and adaptive immunity are glycoproteins. In numerous examples, the crucial influence of glycosylation on critical steps such as receptor interaction and binding has been demonstrated. In this review, we focus on different glycomics and glycoproteomics approaches and their application for studying protein glycosylation in the immune system.

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The plant immune system

The plant immune system | N-Glyco & Plasma membrane Proteomics in Plants | Scoop.it

Many plant-associated microbes are pathogens that impair plant growth and reproduction. Plants respond to infection using a two-branched innate immune system. The first branch recognizes and responds to molecules common to many classes of microbes, including non-pathogens. The second responds to pathogen virulence factors, either directly or through their effects on host targets. These plant immune systems, and the pathogen molecules to which they respond, provide extraordinary insights into molecular recognition, cell biology and evolution across biological kingdoms. A detailed understanding of plant immune function will underpin crop improvement for food, fibre and biofuels production.

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UniCarb-DB: a database resource for glycomic discovery

Summary: Glycosylation is one of the most important post-translational modifications of proteins, known to be involved in pathogen recognition, innate immune response and protection of epithelial membranes. However, when compared to the tools and databases available for the processing of high-throughput proteomic data, the glycomic domain is severely lacking. While tools to assist the analysis of mass spectrometry (MS) and HPLC are continuously improving, there are few resources available to support liquid chromatography (LC)–MS/MS techniques for glycan structure profiling. Here, we present a platform for presenting oligosaccharide structures and fragment data characterized by LC–MS/MS strategies. The database is annotated with high-quality datasets and is designed to extend and reinforce those standards and ontologies developed by existing glycomics databases.

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