Glycobioinformatics: current strategies and tools for data mining in MS-based glycoproteomics (Q30578276)

25 June 2017

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title

Glycobioinformatics: current strategies and tools for data mining in MS-based glycoproteomics (English)

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25 June 2017

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Olga V Glinskii

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Vladislav V. Glinsky

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Vladislav V Glinsky

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3

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author name string

Feng Li

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1

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25 June 2017

19 December 2012

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25 June 2017

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25 June 2017

13

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25 June 2017

2

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25 June 2017

341-354

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Interpreting the protein language using proteomics.

25 June 2017

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https://api.crossref.org/works/10.1002%2FPMIC.201200149

Pathogen-mediated posttranslational modifications: A re-emerging field

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201200149

Protein posttranslational modifications: the chemistry of proteome diversifications

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201200149

Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

EUROCarbDB: An open-access platform for glycoinformatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Glycomics hits the big time

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Sialic acids as regulators of molecular and cellular interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Glycosylation diseases: quo vadis?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Exploring genomes for glycosyltransferases.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201200149

Construction of a human glycogene library and comprehensive functional analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Site occupancy and glycan compositional analysis of two soluble recombinant forms of the attachment glycoprotein of Hendra virus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

The impact of glycosylation on the biological function and structure of human immunoglobulins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Glycan-based interactions involving vertebrate sialic-acid-recognizing proteins

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201200149

Glycoproteomics and clinical applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Glycomics: an integrated systems approach to structure-function relationships of glycans

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

N-linked glycan recognition and processing: the molecular basis of endoplasmic reticulum quality control

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Protein quality control in the ER: the recognition of misfolded proteins

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201200149

Oligosaccharyl transferase: gatekeeper to the secretory pathway

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Combining results from lectin affinity chromatography and glycocapture approaches substantially improves the coverage of the glycoproteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

A perspective on the Maillard reaction and the analysis of protein glycation by mass spectrometry: probing the pathogenesis of chronic disease

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Mass spectrometry based glycoproteomics--from a proteomics perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Recent advances in the MS analysis of glycoproteins: Theoretical considerations

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201200149

Chemistry. Mass spectrometry: bottom-up or top-down?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Combined top-down and bottom-up proteomics identifies a phosphorylation site in stem-loop-binding proteins that contributes to high-affinity RNA binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

An integrated top-down and bottom-up strategy for characterization of protein isoforms and modifications

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Glycoproteome study in myocardial lesions serum by integrated mass spectrometry approach: preliminary insights.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Application of LC/MS to proteomics studies: current status and future prospects

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Decoding protein modifications using top-down mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Tandem mass spectrometry strategies for phosphoproteome analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Glycoproteomics based on tandem mass spectrometry of glycopeptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Direct structural assignment of neutral and sialylated N-glycans of glycopeptides using collision-induced dissociation MSn spectral matching

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Analysis of O-glycan heterogeneity in IgA1 myeloma proteins by Fourier transform ion cyclotron resonance mass spectrometry: implications for IgA nephropathy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

The utility of ETD mass spectrometry in proteomic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Elucidation of O-glycosylation structures of the beta-amyloid precursor protein by liquid chromatography-mass spectrometry using electron transfer dissociation and collision induced dissociation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Proteomic analysis of glycosylation: structural determination of N- and O-linked glycans by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Strategies for analysis of glycoprotein glycosylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

New technologies for glycomic analysis: toward a systematic understanding of the glycome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Enzymatic/chemical release of O-glycans allowing MS analysis at high sensitivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

N-glycan moieties of the crustacean egg yolk protein and their glycosylation sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

18O-labeling of N-glycosylation sites to improve the identification of gel-separated glycoproteins using peptide mass mapping and database searching.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

A guided tour of the Trans-Proteomic Pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

A statistical model for identifying proteins by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Advancing glycomics: implementation strategies at the consortium for functional glycomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Integrated mass spectrometry-based analysis of plasma glycoproteins and their glycan modifications

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. New developments in Protein Prospector allow for reliab

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

In-depth analysis of tandem mass spectrometry data from disparate instrument types

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Modification site localization scoring integrated into a search engine.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

N-Glycan structure annotation of glycopeptides using a linearized glycan structure database (GlyDB)

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Automated N-glycopeptide identification using a combination of single- and tandem-MS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Simultaneous and extensive site-specific N- and O-glycosylation analysis in protein mixtures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

N-glycoproteomics - an automated workflow approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Characterization of site-specific O-glycan structures within the mucin-like domain of alpha-dystroglycan from human skeletal muscle

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

One-pipeline approach achieving glycoprotein identification and obtaining intact glycopeptide information by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Comparison of methods for profiling O-glycosylation: Human Proteome Organisation Human Disease Glycomics/Proteome Initiative multi-institutional study of IgA1

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Overview of tandem mass spectrometry (MS/MS) database search algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Shotgun protein identification and quantification by mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Analysis and validation of proteomic data generated by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Bioinformatics and molecular modeling in glycobiology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Prospects for glycoinformatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Glycan family analysis for deducing N-glycan topology from single MS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

GlycoSpectrumScan: fishing glycopeptides from MS spectra of protease digests of human colostrum sIgA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Generation of asparagine-linked glycan structure databases and their use.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

GlycoMiner: a new software tool to elucidate glycopeptide composition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Bioinformatics in glycomics: glycan characterization with mass spectrometric data using SimGlycan

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

STAT: a saccharide topology analysis tool used in combination with tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Congruent strategies for carbohydrate sequencing. 3. OSCAR: an algorithm for assigning oligosaccharide topology from MSn data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Complexities and algorithms for glycan sequencing using tandem mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Automated interpretation of MS/MS spectra of oligosaccharides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

"Glyco-peakfinder"--de novo composition analysis of glycoconjugates

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

A novel two-stage tandem mass spectrometry approach and scoring scheme for the identification of O-GlcNAc modified peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

UniCarb-DB: a database resource for glycomic discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

A systematic approach to protein glycosylation analysis: a path through the maze

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

GlycoCT-a unifying sequence format for carbohydrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

GlycomeDB - integration of open-access carbohydrate structure databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

GLYDE-an expressive XML standard for the representation of glycan structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

UniCarbKB: putting the pieces together for glycomics research

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

Emerging glycomics technologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201200149

21 January 2018

Identifiers

DOI

10.1002/PMIC.201200149

1 reference

25 June 2017

1 reference

PubMed ID

23175233