LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins.


:The GalNAc O-glycosylation on Ser/Thr residues of extracellular proteins has not been well characterized from a proteomics perspective. We previously reported a sialic acid capture-and-release protocol to enrich tryptic N- and O-glycopeptides from human cerebrospinal fluid glycoproteins using nano-LC-ESI-MS/MS with collision-induced dissociation (CID) for glycopeptide characterization. Here, we have introduced peptide N-glycosidase F (PNGase F) pretreatment of CSF samples to remove the N-glycans facilitating the selective characterization of O-glycopeptides and enabling the use of an automated CID-MS(2)/MS(3) search protocol for glycopeptide identification. We used electron-capture and -transfer dissociation (ECD/ETD) to pinpoint the glycosylation site(s) of the glycopeptides, identified as predominantly core-1-like HexHexNAc-O- structure attached to one to four Ser/Thr residues. We characterized 106 O-glycosylations and found Pro residues preferentially in the n - 1, n + 1, and/or n + 3 positions in relation to the Ser/Thr attachment site (n). The characterization of glycans and glycosylation sites in glycoproteins from human clinical samples provides a basis for future studies addressing the biological and diagnostic importance of specific protein glycosylations in relation to human disease.


J Proteome Res


Halim A,Rüetschi U,Larson G,Nilsson J




Has Abstract


2013-02-01 00:00:00












  • Label-Free LC-MS/MS Proteomic Analysis of Cerebrospinal Fluid Identifies Protein/Pathway Alterations and Candidate Biomarkers for Amyotrophic Lateral Sclerosis.

    abstract::Analysis of the cerebrospinal fluid (CSF) proteome has proven valuable to the study of neurodegenerative disorders. To identify new protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis (ALS), we performed comparative proteomic profiling of CSF from sporadic ALS (sALS), healthy control...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Collins MA,An J,Hood BL,Conrads TP,Bowser RP

    更新日期:2015-11-06 00:00:00

  • Quantitative phosphoproteomic analysis of T cell receptor signaling in diabetes prone and resistant mice.

    abstract::Type 1 diabetes, in human patients and NOD mice, results from an immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the a...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Iwai LK,Benoist C,Mathis D,White FM

    更新日期:2010-06-04 00:00:00

  • Large-Scale Identification of N-Glycan Glycoproteins Carrying Lewis x and Site-Specific N-Glycan Alterations in Fut9 Knockout Mice.

    abstract::The Lewis x (Le(x)) structure (Galβ1-4(Fucα1-3)GlcNAc-R) is a carbohydrate epitope comprising the stage-specific embryonic antigen-1 (SSEA-1) and CD15, and it is synthesized by α1,3-fucosyltransferase 9 (Fut9). Fut9 is expressed specifically in the stomach, kidney, brain, and in leukocytes, suggesting a specific funct...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Noro E,Togayachi A,Sato T,Tomioka A,Fujita M,Sukegawa M,Suzuki N,Kaji H,Narimatsu H

    更新日期:2015-09-04 00:00:00

  • Comparative proteomic analysis of primary schwann cells and a spontaneously immortalized schwann cell line RSC 96: a comprehensive overview with a focus on cell adhesion and migration related proteins.

    abstract::Schwann cells (SCs) are the principal glial cells of the peripheral nervous system (PNS). As a result of tissue heterogeneity and difficulties in the isolation and culture of primary SCs, a considerable understanding of SC biology is obtained from SC lines. However, the differences between the primary SCs and SC lines...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Ji Y,Shen M,Wang X,Zhang S,Yu S,Chen G,Gu X,Ding F

    更新日期:2012-06-01 00:00:00

  • Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data.

    abstract::The two key steps for analyzing proteomic data generated by high-resolution MS are database searching and postprocessing. While the two steps are interrelated, studies on their combinatory effects and the optimization of these procedures have not been adequately conducted. Here, we investigated the performance of thre...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Tu C,Sheng Q,Li J,Ma D,Shen X,Wang X,Shyr Y,Yi Z,Qu J

    更新日期:2015-11-06 00:00:00

  • Automated querying and identification of novel peptides using MALDI mass spectrometric imaging.

    abstract::MSI is a molecular imaging technique that allows for the generation of topographic 2D maps for various endogenous and some exogenous molecules without prior specification of the molecule. In this paper, we start with the premise that a region of interest (ROI) is given to us based on preselected morphological criteria...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Bruand J,Sistla S,Mériaux C,Dorrestein PC,Gaasterland T,Ghassemian M,Wisztorski M,Fournier I,Salzet M,Macagno E,Bafna V

    更新日期:2011-04-01 00:00:00

  • Differentiating proteomic biomarkers in breast cancer by laser capture microdissection and MALDI MS.

    abstract::We assessed proteomic patterns in breast cancer using MALDI MS and laser capture microdissected cells. Protein and peptide expression in invasive mammary carcinoma versus normal mammary epithelium and estrogen-receptor positive versus estrogen-receptor negative tumors were compared. Biomarker candidates were identifie...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Sanders ME,Dias EC,Xu BJ,Mobley JA,Billheimer D,Roder H,Grigorieva J,Dowsett M,Arteaga CL,Caprioli RM

    更新日期:2008-04-01 00:00:00

  • Proteomics of neuroendocrine secretory vesicles reveal distinct functional systems for biosynthesis and exocytosis of peptide hormones and neurotransmitters.

    abstract::Regulated secretory vesicles produce, store, and secrete active peptide hormones and neurotransmitters that function in cell-cell communication. To gain knowledge of the protein systems involved in such secretory vesicle functions, we analyzed proteins in the soluble and membrane fractions of dense core secretory vesi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Wegrzyn J,Lee J,Neveu JM,Lane WS,Hook V

    更新日期:2007-05-01 00:00:00

  • Quantitative phosphoproteomics of tomato mounting a hypersensitive response reveals a swift suppression of photosynthetic activity and a differential role for hsp90 isoforms.

    abstract::An important mechanism by which plants defend themselves against pathogens is the rapid execution of a hypersensitive response (HR). Tomato plants containing the Cf-4 resistance gene mount an HR that relies on the activation of phosphorylation cascades, when challenged with the Avr4 elicitor secreted by the pathogenic...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Stulemeijer IJ,Joosten MH,Jensen ON

    更新日期:2009-03-01 00:00:00

  • Novel proteomic strategy reveal combined alpha1 antitrypsin and cathepsin D as biomarkers for colorectal cancer early screening.

    abstract::Biomarkers for colorectal cancer (CRC) early diagnosis are currently lacking. The purpose of this study was to interpret molecular events in the early stage of CRC that may bring about new biomarkers for early diagnosis. Methylation isotope labeling assistant gel-enhanced liquid chromatography-mass spectrometry (GeLC-...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Xie LQ,Zhao C,Cai SJ,Xu Y,Huang LY,Bian JS,Shen CP,Lu HJ,Yang PY

    更新日期:2010-09-03 00:00:00

  • Identification of novel and cell type enriched cofactors of the transcription activation domain of RelA (p65 NF-kappaB).

    abstract::RelA (NF-kappaB) is a transcription factor inducible by distinct stimuli in many different cell types. To find new cell type specific cofactors of NF-kappaB dependent transcription, we isolated RelA transcription activation domain binding proteins from the nuclear extracts of three different cell types. Analysis by el...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Owen HR,Quadroni M,Bienvenut W,Buerki C,Hottiger MO

    更新日期:2005-07-01 00:00:00

  • Changes in the striatal proteome of YAC128Q mice exhibit gene-environment interactions between mutant huntingtin and manganese.

    abstract::Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG repeat within the Huntingtin (HTT) gene, though the clinical presentation of disease and age-of-onset are strongly influenced by ill-defined environmental factors. We recently reported a gene-environment interaction wherein expressi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Wegrzynowicz M,Holt HK,Friedman DB,Bowman AB

    更新日期:2012-02-03 00:00:00

  • Quantitative Proteomics Reveals Potential Crosstalk between a Small RNA CoaR and a Two-Component Regulator Slr1037 in Synechocystis sp. PCC6803.

    abstract::Bacterial small RNAs (sRNAs) and two-component systems (TCSs) were two vital regulatory mechanisms employed by microorganisms to respond to environmental changes and stresses. As a promising "autotrophic cell factory", photosynthetic cyanobacteria have attracted a lot of attention these years. Although most studies fo...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Sun T,Chen L,Zhang W

    更新日期:2017-08-04 00:00:00

  • Methamphetamine-induced sensitization is associated with alterations to the proteome of the prefrontal cortex: implications for the maintenance of psychotic disorders.

    abstract::Repeat administration of psychostimulants, such as methamphetamine, produces a progressive increase in locomotor activity (behavioral sensitization) in rodents that is believed to represent the underlying neurochemical changes driving psychoses. Alterations to the prefrontal cortex (PFC) are suggested to mediate the e...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Wearne TA,Mirzaei M,Franklin JL,Goodchild AK,Haynes PA,Cornish JL

    更新日期:2015-01-02 00:00:00

  • Prediction of membrane protein types in a hybrid space.

    abstract::Prediction of the types of membrane proteins is of great importance both for genome-wide annotation and for experimental researchers to understand proteins' functions. We describe a new strategy for the prediction of the types of membrane proteins using the Nearest Neighbor Algorithm. We introduced a bipartite feature...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Jia P,Qian Z,Feng K,Lu W,Li Y,Cai Y

    更新日期:2008-03-01 00:00:00

  • Quantitative proteomic analysis of membrane proteins involved in astroglial differentiation of neural stem cells by SILAC labeling coupled with LC-MS/MS.

    abstract::Membrane proteins play a critical role in the process of neural stem cell self-renewal and differentiation. Here, we apply the SILAC (stable isotope labeling by amino acids in cell culture) approach to quantitatively compare the membrane proteome of the self-renewing and the astroglial differentiating cells. High-reso...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Cao R,Chen K,Song Q,Zang Y,Li J,Wang X,Chen P,Liang S

    更新日期:2012-02-03 00:00:00

  • Distinct Gut Microbiota and Serum Metabolites in Response to Weight Loss Induced by Either Dairy or Exercise in a Rodent Model of Obesity.

    abstract::Energy imbalance is a primary cause of obesity. While the classical approach to attenuate weight gain includes an increase in energy expenditure through exercise, dietary manipulation such as the inclusion of dairy products has also been proven effective. In the present study, we explored the potential mechanisms by w...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Mayengbam S,Mickiewicz B,Trottier SK,Mu C,Wright DC,Reimer RA,Vogel HJ,Shearer J

    更新日期:2019-11-01 00:00:00

  • Implementation of an algorithm for modeling disulfide bond patterns using mass spectrometry.

    abstract::The paper describes the implementation of a software system based on the Fenyö disulfide bond assignment algorithm. The system allows an investigator to enter data derived from mass spectrum peak assignments, a target protein sequence and other experimental conditions. The output of the system is the set of disulfide ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Craig R,Krokhin O,Wilkins J,Beavis RC

    更新日期:2003-11-01 00:00:00

  • Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags.

    abstract::Mass spectrometry (MS) has become an accessible tool for whole proteome quantitation with the ability to characterize protein expression across thousands of proteins within a single experiment. A subset of MS quantification methods (e.g., SILAC and label-free) monitor the relative intensity of intact peptides, where t...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: O'Brien JJ,O'Connell JD,Paulo JA,Thakurta S,Rose CM,Weekes MP,Huttlin EL,Gygi SP

    更新日期:2018-01-05 00:00:00

  • Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach.

    abstract::Target-decoy approach (TDA) is the dominant strategy for false discovery rate (FDR) estimation in mass-spectrometry-based proteomics. One of its main applications is direct FDR estimation based on counting of decoy matches above a certain score threshold. The corresponding equations are widely employed for filtering o...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Levitsky LI,Ivanov MV,Lobas AA,Gorshkov MV

    更新日期:2017-02-03 00:00:00

  • Pseudogene recoding revealed from proteomic analysis of salmonella serovars.

    abstract::Recoding refers to the reprogramming of mRNA translation by nonstandard read-out rules. In this study, we used stable isotope labeling with amino acids in cell culture (SILAC) technology to investigate the proteome of host-adapted Salmonella serovars, which are characteristic of accumulation of pseudogenes. Interestin...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Feng Y,Chien KY,Chen HL,Chiu CH

    更新日期:2012-03-02 00:00:00

  • Special Enrichment Strategies Greatly Increase the Efficiency of Missing Proteins Identification from Regular Proteome Samples.

    abstract::As part of the Chromosome-Centric Human Proteome Project (C-HPP) mission, laboratories all over the world have tried to map the entire missing proteins (MPs) since 2012. On the basis of the first and second Chinese Chromosome Proteome Database (CCPD 1.0 and 2.0) studies, we developed systematic enrichment strategies t...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Su N,Zhang C,Zhang Y,Wang Z,Fan F,Zhao M,Wu F,Gao Y,Li Y,Chen L,Tian M,Zhang T,Wen B,Sensang N,Xiong Z,Wu S,Liu S,Yang P,Zhen B,Zhu Y,He F,Xu P

    更新日期:2015-09-04 00:00:00

  • Modulation of colon cancer by nutmeg.

    abstract::Colon cancer is the most common cancer and the third leading cause of cancer mortality in humans. Using mass spectrometry-based metabolomics, the current study revealed the accumulation of four uremic toxins (cresol sulfate, cresol glucuronide, indoxyl sulfate, and phenyl sulfate) in the serum of mice harboring adenom...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Li F,Yang XW,Krausz KW,Nichols RG,Xu W,Patterson AD,Gonzalez FJ

    更新日期:2015-04-03 00:00:00

  • Protein profiling of human pancreatic islets by two-dimensional gel electrophoresis and mass spectrometry.

    abstract::Completion of the human genome sequence has provided scientists with powerful resources with which to explore the molecular events associated with disease states such as diabetes. Understanding the relative levels of expression of gene products, especially of proteins, and their post-translational modifications will b...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Ahmed M,Forsberg J,Bergsten P

    更新日期:2005-05-01 00:00:00

  • Metabolomic Profiling of the Aqueous Humor in Patients with Wet Age-Related Macular Degeneration Using UHPLC-MS/MS.

    abstract::Assessing metabolomic alterations in age-related macular degeneration (AMD) can provide insights into its pathogenesis. We compared the metabolomic profiles of the aqueous humor between wet AMD patients (n = 26) and age- and sex-matched patients undergoing cataract surgery without AMD as controls (n = 20). A global un...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Han G,Wei P,He M,Teng H,Chu Y

    更新日期:2020-06-05 00:00:00

  • ¹H NMR metabolic profiling of plasma reveals additional phenotypes in knockout mouse models.

    abstract::The International Mouse Phenotyping Consortium program has been established to ascribe biological functions to systematically knocked-out (KO) genes by in vivo and ex vivo phenotyping. The plasma clinical chemistry screen includes an assessment of liver, kidney, and bone function and provides a basic lipid profile and...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Probert F,Rice P,Scudamore CL,Wells S,Williams R,Hough TA,Cox IJ

    更新日期:2015-05-01 00:00:00

  • Proteome reference map and comparative proteomic analysis between a wild type Clostridium acetobutylicum DSM 1731 and its mutant with enhanced butanol tolerance and butanol yield.

    abstract::The solventogenic bacterium Clostridium acetobutylicum is an important species of the Clostridium community. To develop a fundamental tool that is useful for biological studies of C. acetobutylicum, we established a high resolution proteome reference map for this species. We identified 1206 spots representing 564 diff...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Mao S,Luo Y,Zhang T,Li J,Bao G,Zhu Y,Chen Z,Zhang Y,Li Y,Ma Y

    更新日期:2010-06-04 00:00:00

  • N-linked glycoproteomic analysis of formalin-fixed and paraffin-embedded tissues.

    abstract::Formalin-fixed, paraffin-embedded (FFPE) tissues have been used to discover disease-associated protein changes using mass spectrometry. Protein post-translational modifications such as glycosylation are known to associate with disease development. In this study, we investigated whether FFPE tissues preserve such modif...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Tian Y,Gurley K,Meany DL,Kemp CJ,Zhang H

    更新日期:2009-04-01 00:00:00

  • Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion.

    abstract::The complete and specific proteolytic cleavage of protein samples into peptides is crucial for the success of every shotgun LC-MS/MS experiment. In particular, popular peptide-based label-free and targeted mass spectrometry approaches rely on efficient generation of fully cleaved peptides to ensure accurate and sensit...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Glatter T,Ludwig C,Ahrné E,Aebersold R,Heck AJ,Schmidt A

    更新日期:2012-11-02 00:00:00

  • XINA: A Workflow for the Integration of Multiplexed Proteomics Kinetics Data with Network Analysis.

    abstract::Quantitative proteomics experiments, using for instance isobaric tandem mass tagging approaches, are conducive to measuring changes in protein abundance over multiple time points in response to one or more conditions or stimulations. The aim is often to determine which proteins exhibit similar patterns within and acro...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Lee LH,Halu A,Morgan S,Iwata H,Aikawa M,Singh SA

    更新日期:2019-02-01 00:00:00