Highly Efficient Identification of O-GalNAc Glycosylation by an Acid-Assisted Glycoform Simplification Approach.

Abstract:

:Compared with N-linked glycosylation, the analysis of O-GalNAc glycosylation is extremely challenging due to the high structure diversity of glycans and lack of glycosidases to release O-GalNAc glycans. In this work, a glycoform simplification strategy by combining HILIC enrichment with chemical de-sialylation to characterize O-GalNAc glycosylation of human serum is presented. This method is first validated by using the bovine fetuin as the test sample. It is found that more than 90% of the sialic acid residues can be removed from bovine fetuin by the acid-assisted de-sialylation method, which significantly simplifies the glycan structure and improves identification sensitivity. Indeed, the number of identified peptide backbones increases nearly one fold when this strategy is used. This method is further applied to analyze the human serum sample, where 185 O-GalNAc modified peptide sequences corresponding to 94 proteins with high confidence (FDR (false detection rate) <1%) are identified. This straight forward strategy can significantly reduce the variations of glycan structures, and is applicable to analysis of other biological samples with high complexity.

journal_name

Proteomics

journal_title

Proteomics

authors

You X,Qin H,Mao J,Tian Y,Dong M,Guo Z,Liang X,Wang L,Jin Y,Ye M

doi

10.1002/pmic.201800042

subject

Has Abstract

pub_date

2018-09-01 00:00:00

pages

e1800042

issue

17

eissn

1615-9853

issn

1615-9861

journal_volume

18

pub_type

杂志文章
  • ICPLQuant - A software for non-isobaric isotopic labeling proteomics.

    abstract::The main goal of many proteomics experiments is an accurate and rapid quantification and identification of regulated proteins in complex biological samples. The bottleneck in quantitative proteomics remains the availability of efficient software to evaluate and quantify the tremendous amount of mass spectral data acqu...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200900174

    authors: Brunner A,Keidel EM,Dosch D,Kellermann J,Lottspeich F

    更新日期:2010-01-01 00:00:00

  • Sample preparation method for isolation of single-cell types from mouse liver for proteomic studies.

    abstract::It becomes increasingly clear that separation of pure cell populations provides a uniquely sensitive and accurate approach to protein profiling in biological systems and opens up a new area for proteomic analysis. The method we described could simultaneously isolate population of hepatocytes (HCs), hepatic stellate ce...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201100157

    authors: Liu W,Hou Y,Chen H,Wei H,Lin W,Li J,Zhang M,He F,Jiang Y

    更新日期:2011-09-01 00:00:00

  • Isobaric Tag-Based Protein Profiling across Eight Human Cell Lines Using High-Field Asymmetric Ion Mobility Spectrometry and Real-Time Database Searching.

    abstract::A vast number of human cell lines are available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, the authors determine the relative protein abundance profiles of a panel of eight diverse, but commonly studied h...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.202000218

    authors: Liu X,Gygi SP,Paulo JA

    更新日期:2021-01-01 00:00:00

  • An integrative proteome analysis of different seedling organs in tolerant and sensitive wheat cultivars under drought stress and recovery.

    abstract::Roots, leaves, and intermediate sections between roots and leaves (ISRL) of wheat seedlings show different physiological functions at the protein level. We performed the first integrative proteomic analysis of different tissues of the drought-tolerant wheat cultivar Hanxuan 10 (HX-10) and drought-sensitive cultivar Ch...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201400179

    authors: Hao P,Zhu J,Gu A,Lv D,Ge P,Chen G,Li X,Yan Y

    更新日期:2015-05-01 00:00:00

  • Quantitative proteomic analysis of HIV-1 Tat-induced dysregulation in SH-SY5Y neuroblastoma cells.

    abstract::Despite affecting up to 70% of HIV-positive patients and being the leading cause of dementia in patients under 40 years, the molecular mechanisms involved in the onset of HIV-associated neurocognitive disorders (HAND) are not well understood. To address this, we performed SILAC-based quantitative proteomic analysis on...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201600236

    authors: Ganief T,Gqamana P,Garnett S,Hoare J,Stein DJ,Joska J,Soares N,Blackburn JM

    更新日期:2017-03-01 00:00:00

  • Protein profiling of epidermal bladder cells from the halophyte Mesembryanthemum crystallinum.

    abstract::Plant epidermal trichomes are as varied in morphology as they are in function. In the halophyte Mesembryanthemum crystallinum, specialized trichomes called epidermal bladder cells (EBC) line the surface of leaves and stems, and increase dramatically in size and volume upon plant salt-treatment. These cells have been p...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201200152

    authors: Barkla BJ,Vera-Estrella R,Pantoja O

    更新日期:2012-09-01 00:00:00

  • Mechanisms of kidney repair by human mesenchymal stromal cells after ischemia: a comprehensive view using label-free MS(E).

    abstract::Acute kidney injury (AKI) is one of the more frequent and lethal pathological conditions seen in intensive care units. Currently available treatments are not totally effective but stem cell-based therapies are emerging as promising alternatives, especially the use of mesenchymal stromal cells (MSC), although the signa...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201300084

    authors: da Costa MR,Pizzatti L,Lindoso RS,Sant'Anna JF,DuRocher B,Abdelhay E,Vieyra A

    更新日期:2014-06-01 00:00:00

  • Stable Protein Gel Storage in Acetonitrile for Mass Spectrometric Analysis.

    abstract::Long-term storage of protein samples for transportation is a challenge in the field of mass spectrometric analysis because the low temperature condition is not easy to be maintained. Here we introduce a simple method to preserve proteins at room temperature for at least one month. In this method, the protein sample is...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201700336

    authors: Chen Y,Wang S,Jia J,Tian X,Xu H,Ning M,Bai B

    更新日期:2018-07-01 00:00:00

  • A DIGE approach for the assessment of rat soleus muscle changes during unloading: effect of acetyl-L-carnitine supplementation.

    abstract::After hind limb suspension, a remodeling of postural muscle phenotype is observed. This remodeling results in a shift of muscle profile from slow-oxidative to fast-glycolytic. These metabolic changes and fiber type shift increase muscle fatigability. Acetyl-L-carnitine (ALCAR) influences the skeletal muscle phenotype ...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200701176

    authors: Moriggi M,Cassano P,Vasso M,Capitanio D,Fania C,Musicco C,Pesce V,Gadaleta MN,Gelfi C

    更新日期:2008-09-01 00:00:00

  • Lipid particle composition of the yeast Yarrowia lipolytica depends on the carbon source.

    abstract::Lipid particles (LP) of all types of cells are a depot of neutral lipids. The present investigation deals with the isolation of LP from the yeast Yarrowia lipolytica and the characterization of their lipid and protein composition. Properties of LP varied depending on the carbon source. LP from glucose-grown cells reve...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500339

    authors: Athenstaedt K,Jolivet P,Boulard C,Zivy M,Negroni L,Nicaud JM,Chardot T

    更新日期:2006-03-01 00:00:00

  • Identification of tumor-associated plasma biomarkers using proteomic techniques: from mouse to human.

    abstract::In an effort to identify tumor-associated proteins from plasma of tumor-bearing mice that may be used as diagnostic biomarkers, we developed a strategy that combines a tumor xenotransplantation model in nude mice with comparative proteomic technology. Five human cancer cell lines (SC-M1, HONE-1, CC-M1, OECM1, GBM 8401...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200400785

    authors: Juan HF,Chen JH,Hsu WT,Huang SC,Chen ST,Yi-Chung Lin J,Chang YW,Chiang CY,Wen LL,Chan DC,Liu YC,Chen YJ

    更新日期:2004-09-01 00:00:00

  • Proteomic profiling for cancer progression: Differential display analysis for the expression of intracellular proteins between regressive and progressive cancer cell lines.

    abstract::Tumor development and progression consist of a series of complex processes involving multiple changes in gene expression (Paolo et al. Physiol. Rev., 1993, 73, 161-195; Lance et al. Cell., 1991, 64, 327-336). Tumor cells acquire an invasive and metastatic phenotype that is the main cause of death for cancer patients. ...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200401132

    authors: Hayashi E,Kuramitsu Y,Okada F,Fujimoto M,Zhang X,Kobayashi M,Iizuka N,Ueyama Y,Nakamura K

    更新日期:2005-03-01 00:00:00

  • Multiwell in-gel protein digestion and microscale sample preparation for protein identification by mass spectrometry.

    abstract::In-gel peptide digestion has become a widely used technique for characterizing proteins resolved by two-dimensional gel electrophoresis. Peptides generated from gel pieces are frequently contaminated with detergent and salts. Prior to matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysi...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/1615-9861(200202)2:2<145::aid-prot145>3.0.

    authors: Pluskal MG,Bogdanova A,Lopez M,Gutierrez S,Pitt AM

    更新日期:2002-02-01 00:00:00

  • Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis.

    abstract::The use of isobaric tags such as iTRAQ allows the relative and absolute quantification of hundreds of proteins in a single experiment for up to eight different samples. More classical techniques such as 2-DE can offer a complimentary approach for the analysis of complex protein samples. In this study, the proteomes of...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200900836

    authors: Mehaffy C,Hess A,Prenni JE,Mathema B,Kreiswirth B,Dobos KM

    更新日期:2010-05-01 00:00:00

  • Temozolomide-modulated glioma proteome: role of interleukin-1 receptor-associated kinase-4 (IRAK4) in chemosensitivity.

    abstract::The current treatment for glioblastoma includes temozolomide (TMZ) chemotherapy, yet the mechanism of action of TMZ is not thoroughly understood. Here, we investigated the TMZ-induced changes in the proteome of the glioma-derived cell line (U251) by 2D DIGE. We found 95 protein spots to be significantly altered in the...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201200261

    authors: Kumar DM,Patil V,Ramachandran B,Nila MV,Dharmalingam K,Somasundaram K

    更新日期:2013-07-01 00:00:00

  • Analysis of human blood serum using the off-line coupling of capillary isoelectric focusing to matrix-assisted laser desorption/ionization time of flight mass spectrometry.

    abstract::Off-line coupling of capillary IEF (CIEF) with matrix-assisted laser desorption/ionization mass spectrometry was utilized for the analysis of human blood serum. Serum proteins were initially separated by CIEF, and fractions of the isoelectric separation were eluted sequentially to a MALDI-TOF MS sample target. During ...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200401212

    authors: Crowley TA,Hayes MA

    更新日期:2005-09-01 00:00:00

  • Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1.

    abstract::CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201800438

    authors: Mehnert M,Li W,Wu C,Salovska B,Liu Y

    更新日期:2019-07-01 00:00:00

  • Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides.

    abstract::CID has become a routine method for fragmentation of peptides in shotgun proteomics, whereas electron transfer dissociation (ETD) has been described as a preferred method for peptides carrying labile PTMs. Though both of these fragmentation techniques have their obvious advantages, they also have their own drawbacks. ...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201000547

    authors: Kim MS,Zhong J,Kandasamy K,Delanghe B,Pandey A

    更新日期:2011-06-01 00:00:00

  • Updating In Vivo and In Vitro Phosphorylation and Methylation Sites of Voltage-Gated Kv7.2 Potassium Channels.

    abstract::Voltage-gated Kv7.2 potassium channels regulate neuronal excitability. The gating of these channels is tightly controlled by various mediators and neurotransmitters acting via G protein-coupled receptors; the underlying signaling cascades involve phosphatidylinositol-4,5-bisphosphate (PIP2 ), Ca2+ /calmodulin, and pho...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201700015

    authors: Erdem FA,Salzer I,Heo S,Chen WQ,Jung G,Lubec G,Boehm S,Yang JW

    更新日期:2017-10-01 00:00:00

  • A proteomic approach to cisplatin resistance in the cervix squamous cell carcinoma cell line A431.

    abstract::Since drug resistance is a complex and multifactorial event involving activation/repression of multiple biochemical pathways, we used a proteomic approach to study cisplatin resistance and drug response in human tumor cell lines. The cervix squamous cell carcinoma cell line A431 and its cisplatin-resistant subline, A4...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200400835

    authors: Castagna A,Antonioli P,Astner H,Hamdan M,Righetti SC,Perego P,Zunino F,Righetti PG

    更新日期:2004-10-01 00:00:00

  • Proteomic analysis reveals a novel role for the actin cytoskeleton in vincristine resistant childhood leukemia--an in vivo study.

    abstract::Intrinsic or acquired resistance to vincristine (VCR), an antimicrotubule agent used in the treatment of childhood acute lymphoblastic leukemia (ALL), is a major clinical problem. Using a clinically relevant NOD/SCID mouse xenograft model of ALL, we established that alterations in the actin and tubulin cytoskeleton ar...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500417

    authors: Verrills NM,Liem NL,Liaw TY,Hood BD,Lock RB,Kavallaris M

    更新日期:2006-03-01 00:00:00

  • A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards.

    abstract::The accurate and precise absolute abundance of proteins can be determined using mass spectrometry by spiking the sample with stable isotope-labeled standards. In this study, we developed a strategy of hierarchical use of peptide-concatenated standards (PCSs) to quantify more proteins over a wider dynamic range. Multip...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201500414

    authors: Kito K,Okada M,Ishibashi Y,Okada S,Ito T

    更新日期:2016-05-01 00:00:00

  • New iodo-acetamido cyanines for labeling cysteine thiol residues. A strategy for evaluating plasma proteins and their oxido-redox status.

    abstract::Two new iodoacetamide-substituted cyanines, C3NIASO3 and C5NIASO3, were synthesized starting from hemicyanine and were utilized for labeling plasma proteins. Specificity, sensitivity and feasibility for SH residues was tested utilizing an equimolar mixture of standard proteins and with normal plasma. Oxidized plasma p...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200800254

    authors: Bruschi M,Grilli S,Candiano G,Fabbroni S,Della Ciana L,Petretto A,Santucci L,Urbani A,Gusmano R,Scolari F,Ghiggeri GM

    更新日期:2009-01-01 00:00:00

  • Differential protein expression in the metal-reducing bacterium Geobacter sulfurreducens strain PCA grown with fumarate or ferric citrate.

    abstract::Geobacter sulfurreducens, generally considered to be a strict anaerobe, is a predominant microbe in subsurface environments, where it utilizes available metals as electron acceptors. To better understand the metabolic processes involved in the metal-reduction capability of this microbe, the proteins expressed by cells...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500137

    authors: Khare T,Esteve-Núñez A,Nevin KP,Zhu W,Yates JR 3rd,Lovley D,Giometti CS

    更新日期:2006-01-01 00:00:00

  • A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva.

    abstract::Head and neck cancers, including oral squamous cell carcinoma (OSCC), are the sixth most common malignancy in the world and are characterized by poor prognosis and a low survival rate. Saliva is oral fluid with intimate contact with OSCC. Besides non-invasive, simple, and rapid to collect, saliva is a potential source...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201500224

    authors: Kawahara R,Bollinger JG,Rivera C,Ribeiro AC,Brandão TB,Paes Leme AF,MacCoss MJ

    更新日期:2016-01-01 00:00:00

  • Autosomal Tubulointerstitial Kidney Disease-MUC1 Type: Differential Proteomics Suggests that Mutated MUC1 (insC) Affects Vesicular Transport in Renal Epithelial Cells.

    abstract::Autosomal dominant tubulointerstitial kidney disease associated to the MUC1 gene (ADTKD-MUC1; formerly MCKD1) belongs to a heterogeneous group of rare hereditary kidney diseases that is prototypically caused by frameshift mutations in the MUC1 repeat domain. The mutant MUC1 (insC) lacks the transmembrane domaine, exhi...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201700456

    authors: Staubach S,Wenzel A,Beck BB,Rinschen MM,Müller S,Hanisch FG

    更新日期:2018-04-01 00:00:00

  • DNA-Barcoded Fluorescence Microscopy for Spatial Omics.

    abstract::Innovation in genomics, transcriptomics, and proteomics research has created a plethora of state-of-the-art techniques such as nucleic acid sequencing and mass-spectrometry-based proteomics with paramount impact in the life sciences. While current approaches yield quantitative abundance analysis of biomolecules on an ...

    journal_title:Proteomics

    pub_type: 杂志文章,评审

    doi:10.1002/pmic.201900368

    authors: Schueder F,Unterauer EM,Ganji M,Jungmann R

    更新日期:2020-10-08 00:00:00

  • Proteomic analysis of the maternal protein restriction rat model for schizophrenia: identification of translational changes in hormonal signaling pathways and glutamate neurotransmission.

    abstract::Previous studies have found that some first onset schizophrenia patients show signs of impaired insulin signaling. Also, epidemiological studies have shown that periods of suboptimal nutrition including protein deficiencies during pregnancy can lead to increased incidence of metabolic conditions and psychiatric disord...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201200376

    authors: Guest PC,Urday S,Ma D,Stelzhammer V,Harris LW,Amess B,Pietsch S,Oheim C,Ozanne SE,Bahn S

    更新日期:2012-12-01 00:00:00

  • Heterogeneous data integration by tree-augmented naïve Bayes for protein-protein interactions prediction.

    abstract::Most proteins execute their functions through interacting with other proteins. Thus, understanding protein-protein interactions (PPIs) is essential to decipher biological functions in a living cell. To predict large-scale PPIs, effective and efficient computational approaches are desirable to integrate heterogeneous d...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.201200326

    authors: Lin X,Chen XW

    更新日期:2013-01-01 00:00:00

  • Rapid protein identification using monolithic enzymatic microreactor and LC-ESI-MS/MS.

    abstract::A monolithic enzymatic microreactor was prepared in a fused-silica capillary by in situ polymerization of acrylamide, glycidyl methacrylate (GMA) and ethylene dimethacrylate (EDMA) in the presence of a binary porogenic mixture of dodecanol and cyclohexanol, followed by ammonia solution treatment, glutaraldehyde activa...

    journal_title:Proteomics

    pub_type: 杂志文章

    doi:10.1002/pmic.200500234

    authors: Duan J,Liang Z,Yang C,Zhang J,Zhang L,Zhang W,Zhang Y

    更新日期:2006-01-01 00:00:00