LC-MS/MS analysis of maize seedling leaf bases
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 480
ORGANISM(S): Zea Mays (maize)
TISSUE(S): Leaf
SUBMITTER: 
Wen-Qiang Wu
LAB HEAD: Chun-Peng Song
PROVIDER: PXD041642 | Pride | 2023-07-24
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| QualIDs.xlsx | Xlsx | |||
| QuanIDs.xlsx | Xlsx | |||
| TR1.raw | Raw | |||
| TR1.xlsx | Xlsx | |||
| TR2.raw | Raw |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:Large-scale identification of N-linked intact glycopeptides by liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) in human serum is challenging due to the wide dynamic range of serum protein abundances, the lack of a complete serum N-Glycan database and the existence of non-specifically digested peptides and numerous modifications. In this regard, a spectral library search method was presented for serum N-linked intact glycopeptides identification with target-decoy and motif-specific false discovery rate (FDR) control. Low-abundant glycoproteins were firstly separated from high-abundant proteins by acetonitrile (ACN) precipitation. After digestion, the N-linked intact glycopeptides were enriched by hydrophilic interaction liquid chromatography (HILIC) column and a portion of the enriched N-linked intact glycopeptides were processed by N-Glycosidase F (PNGase F) to generate de-glycopeptides. Both N-linked intact glycopeptides and de-glycopeptides were analyzed by LC-MS/MS. From N-linked de-glycopeptides datasets, 764 N-linked glycoproteins, 1,699 N-linked glycosites and 3,328 unique N-linked de-glycopeptides were identified. The spectra of these N-linked de-glycopeptides were utilized for N-linked de-glycopeptides library construction and identification of N-linked intact glycopeptides. Four types of N-linked glycosylation motifs (NXS/T/C/V, X≠P) were used to recognize the N-linked de-glycopeptides, and two different N-Glycan mass databases including 27 modified N-Glycan masses and 712 unmodified N-Glycan masses were combined and utilized during spectral library search for identification of N-linked intact glycopeptides. In total, from the N-linked intact glycopeptides datasets, 526 N-linked glycoproteins, 1,036 N-linked glycosites, 22,677 N-linked intact glycopeptides and 738 N-Glycan masses were identified under 1% FDR, representing the most in-depth serum N-glycoproteome identified by LC-MS/MS at N-linked intact glycopeptide level and N-linked de-glycopeptides level.
2020-04-21 | PXD015622 | Pride
Project description:With the optional setting of multiple stepped collisional energies (NCEs), higher-energy collisional dissociation (HCD) as available on Orbitrap instruments is a widely adopted dissociation method for intact N-glycopeptide characterization, where peptide backbones and N-glycan moieties are selectively fragmented at high and low NCEs, respectively. Initially, a dependent setting of a central value plus minus a variation is available to the users to set up NCEs, and the combination of 30±10% to give the energies 20%/30%/40% has been mostly adopted in the literature. With the recent availability of independent NCE setup, we found that the combination of 20%/30%/30% is better than 20%/30%/40%; in the analysis of complex intact N-glycopeptides enriched from gastric cancer tissues, total IDs with spectrum-level FDR≤1%, site-specific IDs with site-determining fragment ions and structure-specific IDs with structure-diagnostic fragment ions were increased by 42% (4,767->6,746), 57% (599->942), and 97% (1771->3495), respectively. This finding will benefit all the coming N-glycoproteomics studies using HCD as the dissociation method.
2020-05-11 | PXD016865 | Pride
Project description:We aimed to in-depth characterize and quantify salivary N-glycoproteomics. HILIC enrichment and LC-MS/MS were combined to investigate salivary glycosylation both at deglycopeptides level and glycopepeptides level, and alterations in site-specific glycoforms for human saliva were detected between lung cancer patients and healthy subjects. Firstly, intact glycopeptides were enriched from human saliva through using HILIC. Obtained intact glycopeptides were characterized by LC-MS/MS directly. Furthermore, the glycosylation sites were fully identified by LC-MS/MS followed by incubating with PNGase F. The developed workflow was applied to compare N-glycosites and intact N-glycopeptides in lung cancer group and healthy control group. Dysregulated N-glycosites as well as site-specific glycoforms were confidently observed in lung cancer and their potential value in clinical applications will be discussed.
2023-02-08 | PXD030670 | Pride
Project description:In this study, we used human THP-1-derived macrophages as an immune cell model, and systematically performed glycoproteomics of three subtypes of macrophages by StrucGP.To study the N‑Glycoproteomic of them, the intact glycopeptides were first enriched and identified using triplicate mass spectrometry (MS)-based glycoproteomic approaches, then StrucGP was used for subsequent analysis. In total three subtypes of macrophages, these intact glycopeptides consist of 253 N-linked glycan structures at 652 unique glycosites from 372 N-glycoproteins, along with their PSM information. A total of 135, 163, and 201 N-glycan structures were identified from M0, M1, and M2 macrophages, respectively.
2023-10-19 | PXD030277 | Pride
Project description:Hepatocellular carcinoma (HCC) ranks sixth among the most common malignancies and fourth in mortality among all kinds of cancers in the world. Recent advances in early diagnosis and therapeutics have led to improved survival of HCC patients, but the recurrence and metastasis are still main reasons for the poor prognosis and high mortality of HCC. Many researches on the mechanism of HCC deterioration have uncovered the epithelial-mesenchymal transition (EMT) as a major trigger for HCC metastasis and invasion.In this study, in order to systematically investigate the dynamic site-specific glycosylation alterations associated with the EMT process of HCC, two hepatoma cell lines SMMC-7721 and HepG2 were treated using HGF and the cell proteins were harvested at six treatment time points. Using TMT-labeling, solid phase extraction and mass spectrometry, we not only detailly profiled N-glycoproteome of both cell lines at site-specific glycosylation level, but also dynamically quantified those intact glycopeptides among six increasing HGF-treated time points. By dynamically quantifying enriched glycopeptides and proteins among six HGF-treated time points in two cell lines, we identified 20 up-regulated intact glycopeptides during the process of EMT, with the majority changed at the glycosylation level instead of protein expression level. The site-specific glycosylation change of those glycoproteins was related to the process of EMT, which was further verified by a series of molecular biology methods, mass spectrometry, and migration and invasion assay in vitro.
2021-09-09 | PXD017033 | Pride
Project description:Both SKOV3 and IOSE80 cells were cultured and extracted the proteins. With sequential digestion by trypsin, enriched by Zwitterionic Hydrophilic Interaction chromatography (ZIC-HILIC), the intact N-glycopeptides were then isotopic diethyl labelled and analyzed using C18-RPLC-MS/MS (HCD).
2023-03-10 | PXD030927 | Pride
Project description:Alterations in protein glycosylation, especially the terminal sialylation, are closely correlated with physiological and pathological regulation. Due to the low ionization efficiency of sialo-glycopeptides and frequently observed dissociation of sialic acid residues during mass spectrometry analysis, tools to enrich the sialo-glycopeptides are essential to enhance detection sensitivity and identification efficiency in sialo-glycoproteomics. In this study, we present the first application of zwitterionic hydrophilic interaction chromatography (ZIC-cHILIC) material in StageTip for simultaneous enrichment and fractionation of intact glycopeptides at proteome scale. With the demonstrated enrichment specificity and identification depth, the stepwise-ZIC-cHILIC can be an efficient enrichment method for the discovery of glycosylation sites and native glycotope for many sample types.
2022-02-25 | PXD010456 | Pride
Project description:Intact glycopeptides in MEVs from bovines, caprines, porcines and humans were comprehensively analyzed by high-resolution mass spectrometry using the sceHCD followed by EThcD fragment method, revealing that protein glycosylation is abundant and heterogeneous in MEVs.
2024-01-30 | PXD044641 | Pride
Project description:Benign prostatic hyperplasia (BPH) is difficult to discriminate from prostate carcinoma (PCa) preoperatively. The non-invasive biomarkers are necessary to reduce the burden of biopsies and improve survival quality of patients. Previous research suggests that abnormal glycosylation of immunoglobulin gamma molecules (IgGs) may associated with immunological diseases and prostate diseases. Hence, characterizing intact N-glycopeptides of IgGs that correspond to N-glycan structure with specific site information enable better understanding of the molecular pathogenesis and finding out some novel signatures in preoperative discrimination of BPH from PCa. In this study, we profiled intact N-glycopeptides of purified IgGs from 51 PCa patients and 45 BPH patients by our developed N-glycoproteomic method using hydrophilic interaction liquid chromatography enrichment coupled with high resolution LC-MS/MS, and intact N-glycopeptides quantitative analysis was performed using pGlyco 2.0 and MaxQuant softwares. Our data provided plasma IgG subclass-specific and site-specific N-glycosylation quantitative information.
2020-06-29 | PXD016175 | Pride
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