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Mouse glycoproteome - pGlyco 2

ABSTRACT: Precise and large-scale characterization of glycoproteome is critical for understanding the biological functions of glycoproteins. Due to the complexity of glycosylation, the overall throughput, data quality and accessibility of site-specific glycosylation analysis are overwhelmingly lower than those of routine proteomic studies. Here, we introduce a workflow that robustly identifies intact glycopeptides at a proteome scale using stepped-energy mass-spectrometry (MS) and pGlyco 2.0, a dedicated search engine for large-scale glycopeptide analysis with comprehensive quality control (false discovery rate evaluation on the glycan, peptide and glycopeptide matches).

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Lung

SUBMITTER: pGlyco pFind

LAB HEAD: Mingqi Liu

PROVIDER: PXD005555 | Pride | 2017-10-11

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	MouseLung-Z-T-1-FDR.txt	Txt
	MouseLung-Z-T-1.raw	Raw
	MouseLung-Z-T-2-FDR.txt	Txt
	MouseLung-Z-T-2.raw	Raw
	MouseLung-Z-T-3-FDR.txt	Txt

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Publications

Physiological implications of NTBI uptake by T lymphocytes.

Pinto Jorge P JP Arezes João J Dias Vera V Oliveira Susana S Vieira Inês I Costa Mónica M Vos Matthijn M Carlsson Anna A Rikers Yuri Y Rangel Maria M Porto Graça G

Frontiers in pharmacology 20140226

In iron overload disorders a significant fraction of the total iron circulates in the plasma as low molecular weight complexes not bound to transferrin, known as non-transferrin-bound iron (NTBI). By catalyzing the formation of free radicals, NTBI accumulation results in oxidative stress and cellular damage, being a major cause of organ toxicity. NTBI is rapidly and preferentially cleared from circulation by the liver and the myocardium, the main disease targets in iron overload conditions. We h ...[more]

PMID: 24616700

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Mouse glycoproteome - pGlyco 2

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Glycoproteomics with AI-ETD - Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis

Project description:Protein glycosylation is a highly important, yet a poorly understood protein post-translational modification. Thousands of possible glycan structures and compositions create potential for tremendous site heterogeneity and analytical challenge. A lack of suitable analytical methods for large-scale analyses of intact glycopeptides has ultimately limited our abilities to both address the degree of heterogeneity across the glycoproteome and to understand how it contributes biologically to complex systems. Here we show that N-glycoproteome site-specific microheterogeneity can be captured at a global level via glycopeptide profiling with activated ion electron transfer dissociation (AI-ETD), enabling characterization of nearly 2,100 N-glycosites (> 7,500 unique N-glycopeptides) from mouse brain tissue. Moreover, we have used this unprecedented scale of glycoproteomic data to develop several new visualizations that will prove useful for analyzing intact glycopeptides in future studies. Our data reveal that N-glycosylation profiles can differ between subcellular regions and structural domains and that N-glycosite heterogeneity manifests in several different forms, including dramatic differences in glycosites on the same protein.

2019-04-02 | PXD011533 | Pride

Identification of AMPK phosphorylation sites reveals a network of proteins involved in cell invasion and facilitates large-scale substrate prediction

Project description:AMP-activated protein kinase (AMPK) is a central energy gauge that regulates metabolism and has been increasingly involved in non-metabolic processes and diseases. However, AMPK’s direct substrates in non-metabolic contexts are largely unknown. To better understand the AMPK network, we use a chemical genetics screen coupled to a peptide capture approach in whole cells, resulting in identification of direct AMPK phosphorylation sites. Interestingly, the high-confidence AMPK substrates contain many proteins involved in cell motility, adhesion, and invasion. AMPK phosphorylation of the RHOA guanine nucleotide exchange factor NET1A inhibits extracellular matrix degradation, an early step in cell invasion. The identification of direct AMPK phosphorylation sites also facilitates large-scale prediction of AMPK substrates. We provide an AMPK motif matrix and a pipeline to predict additional AMPK substrates from quantitative phosphoproteomics datasets. As AMPK is emerging as a critical node in aging and pathological processes, our study identifies potential targets for therapeutic strategies.

2015-10-09 | PXD003019 | Pride

SugarQuant: a streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics

Project description:Site-specific regulation of protein N-glycosylation is essential in human cells. However, accurate quantification of glycosylation sites and their individual glycan moieties in a cell-wide manner is still technically challenging. Here, we introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising fast protein aggregation capture (PAC)-based sample preparation, optimized multi-notch MS3 LC-MS acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that allows for confident, global identification and quantification of intact glycopeptides in complex biological samples. PAC greatly reduces the overall sample-handling time without compromising sensitivity. Glyco-SPS-MS3 combines high-resolution MS2 and MS3 scans, resulting in enhanced reporter signals of isobaric mass tags, improved detection of N-glycopeptide fragments, and significantly lowered interference in multiplexed quantification. GlycoBinder enables streamlined processing of Glyco-SPS-MS3 data, followed by a two-step database search which increases the identification rates of intact glycopeptides by up to 22% when compared with one-step database search strategies. SugarQuant was applied to identify and quantify more than 5,000 unique glycoforms in Burkitt’s lymphoma cells, and determined complex site-specific glycosylation changes that occurred upon inhibition of fucosylation at high confidence.

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IMPROVED N- AND O-GLYCOPEPTIDE IDENTIFICATION USING HIGH-FIELD ASYMMETRIC WAVEFORM ION MOBILITY SPECTROMETRY (FAIMS)

Project description:Mass spectrometry is the premier tool for identifying and quantifying site-specific protein glycosylation globally. Analysis of intact glycopeptides often requires an enrichment step, after which the samples remain highly complex and exhibit a broad dynamic range of abundance. Here, we evaluated the analytical benefits of high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to nano-liquid chromatography mass spectrometry (nLC-MS) for analyses of intact glycopeptide devoid of any enrichment step. We compared the effects of compensation voltage on the transmission of N- and O-glycopeptides derived from heterogeneous protein mixtures using two FAIMS devices. We comprehensively demonstrate the performance characteristics of the FAIMS device for glycopeptide analysis and recommend optimal electrode temperature and compensation voltage (CV) settings for N- and O-glycopeptide analysis. Under optimal CV settings, FAIMS-assisted gas-phase fractionation in conjunction with chromatographic reverse phase separation resulted in a 31% increase in the detection of both N- and O-glycopeptide compared to control experiments without FAIMS. Overall, our results demonstrate that FAIMS provides an alternative means to access glycopeptides without any enrichment providing an unbiased global glycoproteome landscape. In addition, our work provides the framework to verify ‘difficult-to-identify’ glycopeptide features.

2023-10-24 | PXD038673 | Pride

SIRT3 interactions and mitochondrial proteome during HCMV infection

Project description:SIRT3 has been shown to inhibit HCMV infection, but the mechanism under the antiviral effect is not clear. To identify the mediator of SIRT3 antiviral function, we aim to identify and quantify SIRT3 interactions during HCMV infection. A set of large-scale IPs were performed to determine the specific interactions with SIRT3 during infection, while small-scale IPs were conducted to determine the temporal interactions over the life cycle of infection. The mitochondrial proteome was used to characterize the changes of protein abundances after infection, and it was used for the normalization of acetylation.

2021-04-01 | PXD018995 | Pride

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