N-linked Glycosylation Enrichment for In-depth Cell Surface Proteomics of Diffuse Large B-cell Lymphoma Subtypes

Deeb, Sally J.; Cox, Juergen; Schmidt-Supprian, Marc; Mann, Matthias

doi:10.1074/mcp.m113.033977

Cited by 84 publications

(77 citation statements)

References 49 publications

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“…Human plasma glycopeptide enrichment was performed with a modified filter-aided protocol [47–49]. Tryptic plasma peptides were loaded onto Microcon filters YM-30 with 80 μL binding buffer (1 mM CaCl 2 , 1 mM MnCl 2 , 0.5 M NaCl in 20 mM TrisHCl, pH 7.3).…”

Section: Methodsmentioning

confidence: 99%

Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization

Wang

Chen

et al. 2017

J. Am. Soc. Mass Spectrom.

186

195

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Protein glycosylation, one of the most heterogeneous post-translational modifications, can play a major role in cellular signal transduction and disease progression. Traditional mass spectrometry (MS)-based large-scale glycoprotein sequencing studies heavily rely on identifying enzymatically released glycans and their original peptide backbone separately, as there is no efficient fragmentation method to produce unbiased glycan and peptide product ions simultaneously in a single spectrum and can be conveniently applied to high throughput glycoproteome characterization, especially for N-glycopeptides which can have much more branched glycan side chains than relatively less complex O-linked glycans. In this study a re-defined electron-transfer/higher-energy collision dissociation (EThcD) fragmentation scheme is applied to incorporate both glycan and peptide fragments in one single spectrum, enabling complete information to be gathered and great microheterogeneity details to be revealed. Fetuin was first utilized to prove the applicability with 19 glycopeptides and corresponding 5 glycosylation sites identified. Subsequent experiments tested its utility for human plasma N-glycoproteins. Large-scale studies explored N-glycoproteomics in rat carotid over the course of restenosis progression to investigate potential role of glycosylation. The integrated fragmentation scheme provides a powerful tool for the analysis of intact N-glycopeptides and N-glycoproteomics. We also anticipate this approach can be readily applied to large-scale O-glycoproteome characterization.

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Section: Methodsmentioning

confidence: 99%

Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization

Wang

Chen

et al. 2017

J. Am. Soc. Mass Spectrom.

186

195

View full text Add to dashboard Cite

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“…The following parameters were specified in the protein database searches: only tryptic peptides with up to two missed cleavage sites were allowed as done previously (Meissner et al , 2013; Deeb et al , 2014); 10 p.p.m. mass tolerances for MS and 0.6Da for MS/MS fragment ions; carbamidomethylcysteine as a fixed modification; and protein N-acetylation, oxidized methionine, and phospho_STY (serine, threonine, and tyrosine) were permitted as variable modifications (Ye et al , 2010 a ).…”

Section: Methodsmentioning

confidence: 99%

Abundant protein phosphorylation potentially regulates Arabidopsis anther development

Zhang

You

et al. 2016

EXBOTJ

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“…Most studies are based on the cell surface capture technology, which covalently labels extracellular glycan moieties on living cells (20). These studies focused for example on the surface proteome of stem cells (21), mesenchymal stromal cells (22), and murine adipocytes in obesity (23) as well as other immune cells such as B cell lines derived from lymphomas (24).…”

Section: Naive Cd4mentioning

confidence: 99%

A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation

Graessel

Hauck

Toerne

et al. 2015

Molecular & Cellular Proteomics

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Naive CD4؉ T cells are the common precursors of multiple effector and memory T-cell subsets and possess a high plasticity in terms of differentiation potential. This stemcell-like character is important for cell therapies aiming at regeneration of specific immunity. Naive CD4ϩ T cells are the common precursors for all other T-helper cell subsets and it is of fundamental importance for specific immunity that their differentiation process is well directed. A complex signaling network is engaged upon antigen recognition that triggers the differentiation process of stemcell-like, plastic, antigen-unexperienced naive T cells into antigen-specific, functional distinct T-cell subphenotypes (1). The differentiation process of naive T cells is tightly regulated in healthy individuals. Pathology develops under dysregulated effector responses such as overshooting responses leading to impaired tolerance (2) or ineffective control of infections (3). Naive T cells are defined by CD45RA expression and they are early cellular targets of immune modulation regarding the differentiation process and the development of long lasting, sustainable therapeutic strategies. In contrast, memory T cells express CD45RO and cover already committed cells such as T helper 1 and T helper 2 cells. Therefore, we chose to investigate the naive CD4 ϩ T cell (CD45RA) and its phenotype during T-cell receptor (TCR) 1 activation. The differentiation From the ‡Center of Allergy and Environment (ZAUM), Technische

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N-linked Glycosylation Enrichment for In-depth Cell Surface Proteomics of Diffuse Large B-cell Lymphoma Subtypes

Cited by 84 publications

References 49 publications

Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization

Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization

Abundant protein phosphorylation potentially regulates Arabidopsis anther development

A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation

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