Liquid chromatography-tandem mass spectrometry-based fragmentation analysis of glycopeptides

[1]  William F. Martin,et al.  Automated glycopeptide analysis - review of current state and future directions , 2013, Briefings Bioinform..

[2]  C. Sihlbom,et al.  Identification of Chondroitin Sulfate Linkage Region Glycopeptides Reveals Prohormones as a Novel Class of Proteoglycans* , 2014, Molecular & Cellular Proteomics.

[3]  Suh-Yuen Liang,et al.  An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry , 2014, Bioinform..

[4]  N. Hashii,et al.  Simultaneous glycosylation analysis of human serum glycoproteins by high-performance liquid chromatography/tandem mass spectrometry. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[5]  W. Ens,et al.  Characterizing degradation products of peptides containing N‐terminal Cys residues by (off‐line high‐performance liquid chromatography)/matrix‐assisted laser desorption/ionization quadrupole time‐of‐flight measurements , 2003, Rapid communications in mass spectrometry : RCM.

[6]  Jonas Nilsson,et al.  Assignment of saccharide identities through analysis of oxonium ion fragmentation profiles in LC-MS/MS of glycopeptides. , 2014, Journal of proteome research.

[7]  T. Rejtar,et al.  Ultrasensitive characterization of site-specific glycosylation of affinity-purified haptoglobin from lung cancer patient plasma using 10 μm i.d. porous layer open tubular liquid chromatography-linear ion trap collision-induced dissociation/electron transfer dissociation mass spectrometry. , 2011, Analytical chemistry.

[8]  Daniel Kolarich,et al.  Determination of site-specific glycan heterogeneity on glycoproteins , 2012, Nature Protocols.

[9]  N. Packer,et al.  Structural analysis of glycoprotein sialylation – Part I: pre-LC-MS analytical strategies , 2013 .

[10]  M. Mann,et al.  Integrated analysis of the cerebrospinal fluid peptidome and proteome. , 2008, Journal of proteome research.

[11]  D. Josić,et al.  Determination of the site‐specific and isoform‐specific glycosylation in human plasma‐derived antithrombin by IEF and capillary HPLC‐ESI‐MS/MS , 2005, Proteomics.

[12]  N. Packer,et al.  Structural analysis of N- and O-glycans released from glycoproteins , 2012, Nature Protocols.

[13]  B. Chait,et al.  Influence of ions on cyclization of the amino terminal glutamine residues of tryptic peptides of streptococcal PepM49 protein. Resolution of cyclized peptides by HPLC and characterization by mass spectrometry. , 2009, International journal of peptide and protein research.

[14]  Targeting the glycoproteome , 2012, Glycoconjugate Journal.

[15]  Henrik Clausen,et al.  Location, location, location: new insights into O-GalNAc protein glycosylation. , 2011, Trends in cell biology.

[16]  Jonas Nilsson,et al.  Characterization of site-specific O-glycan structures within the mucin-like domain of alpha-dystroglycan from human skeletal muscle. , 2010, Glycobiology.

[17]  C. Junot,et al.  Evaluation of a combined glycomics and glycoproteomics approach for studying the major glycoproteins present in biofluids: Application to cerebrospinal fluid. , 2015, Rapid communications in mass spectrometry : RCM.

[18]  I. Rudan,et al.  High-throughput IgG Fc N-glycosylation profiling by mass spectrometry of glycopeptides. , 2013, Journal of proteome research.

[19]  Suh-Yuen Liang,et al.  Sweet-Heart - an integrated suite of enabling computational tools for automated MS2/MS3 sequencing and identification of glycopeptides. , 2013, Journal of proteomics.

[20]  C. Hesse,et al.  Enrichment of glycopeptides for glycan structure and attachment site identification , 2009, Nature Methods.

[21]  H. Wandall,et al.  A Strategy for O-Glycoproteomics of Enveloped Viruses—the O-Glycoproteome of Herpes Simplex Virus Type 1 , 2015, PLoS pathogens.

[22]  F. Altmann,et al.  Comprehensive glyco‐proteomic analysis of human α1‐antitrypsin and its charge isoforms , 2006, Proteomics.

[23]  Marshall Bern,et al.  Glycoproteomic Analysis of the Secretome of Human Endothelial Cells , 2013, Molecular & Cellular Proteomics.

[24]  Nicolle H Packer,et al.  Advances in LC-MS/MS-based glycoproteomics: getting closer to system-wide site-specific mapping of the N- and O-glycoproteome. , 2014, Biochimica et biophysica acta.

[25]  G. Larson,et al.  Synthesis aided structural determination of amyloid-β(1-15) glycopeptides, new biomarkers for Alzheimer's disease. , 2014, Chemical communications.

[26]  André M Deelder,et al.  Site-specific N-glycosylation analysis of human immunoglobulin e. , 2014, Journal of proteome research.

[27]  Lance Wells,et al.  Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment. , 2011, Journal of proteome research.

[28]  Helen J Cooper,et al.  Higher energy collision dissociation (HCD) product ion-triggered electron transfer dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins. , 2012, Journal of proteome research.

[29]  T. Takao,et al.  N‐glycosylation at Asn491 in the Asn‐Xaa‐Cys motif of human transferrin , 2004, FEBS letters.

[30]  M. Mann,et al.  Higher-energy C-trap dissociation for peptide modification analysis , 2007, Nature Methods.

[31]  M F Bean,et al.  Collisional fragmentation of glycopeptides by electrospray ionization LC/MS and LC/MS/MS: methods for selective detection of glycopeptides in protein digests. , 1993, Analytical chemistry.

[32]  Sakari Joenväärä,et al.  N-glycoproteomics - an automated workflow approach. , 2008, Glycobiology.

[33]  G. Larson,et al.  O-Mannose and O-N-acetyl galactosamine glycosylation of mammalian α-dystroglycan is conserved in a region-specific manner. , 2012, Glycobiology.

[34]  L. Musante,et al.  N-linked (N-) Glycoproteomics of Urimary Exosomes* , 2014, Molecular & Cellular Proteomics.

[35]  Nichollas E. Scott,et al.  Site-specific glycan-peptide analysis for determination of N-glycoproteome heterogeneity. , 2013, Journal of proteome research.

[36]  E. Bennett,et al.  O-Glycosylation Modulates Proprotein Convertase Activation of Angiopoietin-like Protein 3 , 2010, The Journal of Biological Chemistry.

[37]  K. Blennow,et al.  Site-specific characterization of threonine, serine, and tyrosine glycosylations of amyloid precursor protein/amyloid β-peptides in human cerebrospinal fluid , 2011, Proceedings of the National Academy of Sciences.

[38]  Y. Mechref,et al.  Quantification of glycopeptides by multiple reaction monitoring liquid chromatography/tandem mass spectrometry. , 2012, Rapid communications in mass spectrometry : RCM.

[39]  Kristy Brown,et al.  Characterization of Transferrin Glycopeptide Structures in Human Cerebrospinal Fluid. , 2012, International journal of mass spectrometry.

[40]  A. G. Semenov,et al.  Processing of pro-brain natriuretic peptide is suppressed by O-glycosylation in the region close to the cleavage site. , 2009, Clinical chemistry.

[41]  Daniel Figeys,et al.  Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method. , 2014, Journal of proteomics.

[42]  Manfred Wuhrer,et al.  Glycomics using mass spectrometry , 2012, Glycoconjugate Journal.

[43]  P. Roepstorff,et al.  Proposal for a common nomenclature for sequence ions in mass spectra of peptides. , 1984, Biomedical mass spectrometry.

[44]  R. Linhardt,et al.  The proteoglycan bikunin has a defined sequence , 2011, Nature chemical biology.

[45]  P. Roepstorff,et al.  Mass spectrometric determination of O-glycosylation sites using beta-elimination and partial acid hydrolysis. , 2001, Analytical chemistry.

[46]  André M Deelder,et al.  Protein glycosylation analysis by HILIC-LC-MS of Proteinase K-generated N- and O-glycopeptides. , 2010, Journal of separation science.

[47]  Robert J. Chalkley,et al.  Tissue-Specific Glycosylation at the Glycopeptide Level* , 2015, Molecular & Cellular Proteomics.

[48]  T. Hayakawa,et al.  Site-specific N-glycosylation analysis of human plasma ceruloplasmin using liquid chromatography with electrospray ionization tandem mass spectrometry. , 2006, Analytical biochemistry.

[49]  A G Marshall,et al.  Electron capture dissociation and infrared multiphoton dissociation MS/MS of an N-glycosylated tryptic peptic to yield complementary sequence information. , 2001, Analytical chemistry.

[50]  Kay-Hooi Khoo,et al.  Human Sperm Binding Is Mediated by the Sialyl-Lewisx Oligosaccharide on the Zona Pellucida , 2011, Science.

[51]  N. Karlsson,et al.  The O-glycomap of Lubricin, a Novel Mucin Responsible for Joint Lubrication, Identified by Site-specific Glycopeptide Analysis , 2014, Molecular & Cellular Proteomics.

[52]  G. Larson,et al.  LC-MS/MS characterization of combined glycogenin-1 and glycogenin-2 enzymatic activities reveals their self-glucosylation preferences. , 2014, Biochimica et biophysica acta.

[53]  C. G. Edmonds,et al.  Tandem mass spectrometry of very large molecules. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization. , 1993, Analytical chemistry.

[54]  F. He,et al.  Efficient and accurate glycopeptide identification pipeline for high-throughput site-specific N-glycosylation analysis. , 2014, Journal of proteome research.

[55]  H. Wandall,et al.  Mining the O-glycoproteome using zinc-finger nuclease–glycoengineered SimpleCell lines , 2011, Nature Methods.

[56]  A. Oldfors,et al.  P4.46 Molecular pathogenesis of a new glycogenosis caused by a mutation in glycogenin-1 , 2010, Neuromuscular Disorders.

[57]  Ulrika Westerlind Synthetic glycopeptides and glycoproteins with applications in biological research , 2012, Beilstein journal of organic chemistry.

[58]  M. F. Bean,et al.  Selective identification and differentiation of N‐and O‐linked oligosaccharides in glycoproteins by liquid chromatography‐mass spectrometry , 1993, Protein science : a publication of the Protein Society.

[59]  G. Larson,et al.  LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins. , 2013, Journal of proteome research.

[60]  J R Yates,et al.  Protein sequencing by tandem mass spectrometry. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[61]  C. Sihlbom,et al.  Positive Mode LC-MS/MS Analysis of Chondroitin Sulfate Modified Glycopeptides Derived from Light and Heavy Chains of The Human Inter-α-Trypsin Inhibitor Complex* , 2015, Molecular & Cellular Proteomics.

[62]  R. Renkonen,et al.  De novo glycan structure search with the CID MS/MS spectra of native N-glycopeptides. , 2009, Glycobiology.

[63]  Erdmann Rapp,et al.  Quantitative mapping of glycoprotein micro-heterogeneity and macro-heterogeneity: an evaluation of mass spectrometry signal strengths using synthetic peptides and glycopeptides. , 2013, Journal of mass spectrometry : JMS.

[64]  W. Ens,et al.  Deamidation of -Asn-Gly- sequences during sample preparation for proteomics: Consequences for MALDI and HPLC-MALDI analysis. , 2006, Analytical chemistry.

[65]  Jonathan C Trinidad,et al.  N- and O-Glycosylation in the Murine Synaptosome* , 2013, Molecular & Cellular Proteomics.

[66]  K. Medzihradszky Characterization of protein N-glycosylation. , 2005, Methods in enzymology.

[67]  Henrik Clausen,et al.  Site-specific protein O-glycosylation modulates proprotein processing - deciphering specific functions of the large polypeptide GalNAc-transferase gene family. , 2012, Biochimica et biophysica acta.

[68]  L. Buhse,et al.  Direct approach for qualitative and quantitative characterization of glycoproteins using tandem mass tags and an LTQ Orbitrap XL electron transfer dissociation hybrid mass spectrometer. , 2013, Analytical chemistry.

[69]  E. Bennett,et al.  O-Linked Glycosylation of the Mucin Domain of the Herpes Simplex Virus Type 1-specific Glycoprotein gC-1 Is Temporally Regulated in a Seed-and-spread Manner* , 2014, The Journal of Biological Chemistry.

[70]  B. Ma,et al.  GlycoMaster DB: software to assist the automated identification of N-linked glycopeptides by tandem mass spectrometry. , 2014, Journal of proteome research.

[71]  C. Sihlbom,et al.  Distinctive MS/MS Fragmentation Pathways of Glycopeptide-Generated Oxonium Ions Provide Evidence of the Glycan Structure. , 2016, Chemistry.

[72]  Alexandre M J J Bonvin,et al.  Extended O-GlcNAc on HLA Class-I-Bound Peptides. , 2015, Journal of the American Chemical Society.

[73]  C. Bertozzi,et al.  Isotope-targeted glycoproteomics (IsoTaG): a mass-independent platform for intact N- and O-glycopeptide discovery and analysis , 2015, Nature Methods.

[74]  H. Wandall,et al.  Precision genome editing: a small revolution for glycobiology. , 2014, Glycobiology.

[75]  Michael Przybylski,et al.  Elucidation of O-glycosylation structures of the beta-amyloid precursor protein by liquid chromatography-mass spectrometry using electron transfer dissociation and collision induced dissociation. , 2009, Journal of proteome research.

[76]  D. Uhrín,et al.  Structural basis for sialic acid-mediated self-recognition by complement factor H. , 2015, Nature chemical biology.

[77]  Naoyuki Taniguchi,et al.  Comparison of the methods for profiling glycoprotein glycans--HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study. , 2007, Glycobiology.

[78]  M. Larsen,et al.  Structural analysis of glycoprotein sialylation – part II: LC-MS based detection , 2013 .

[79]  K. Medzihradszky,et al.  How to Dig Deeper? Improved Enrichment Methods for Mucin Core-1 Type Glycopeptides* , 2012, Molecular & Cellular Proteomics.

[80]  Jeremy C. Collette,et al.  Emerging Paradigms for the Initiation of Mucin-type Protein O-Glycosylation by the Polypeptide GalNAc Transferase Family of Glycosyltransferases* , 2011, The Journal of Biological Chemistry.

[81]  Jonas Nilsson,et al.  Human Urinary Glycoproteomics; Attachment Site Specific Analysis of N- and O-Linked Glycosylations by CID and ECD* , 2011, Molecular & Cellular Proteomics.

[82]  E. Fiebiger,et al.  A single glycan on IgE is indispensable for initiation of anaphylaxis , 2015, The Journal of experimental medicine.

[83]  Nichollas E. Scott,et al.  Simultaneous Glycan-Peptide Characterization Using Hydrophilic Interaction Chromatography and Parallel Fragmentation by CID, Higher Energy Collisional Dissociation, and Electron Transfer Dissociation MS Applied to the N-Linked Glycoproteome of Campylobacter jejuni* , 2010, Molecular & Cellular Proteomics.

[84]  J. J. Conboy,et al.  The determination of glycopeptides by liquid chromatography/mass spectrometry with collision-induced dissociation , 1992, Journal of the American Society for Mass Spectrometry.

[85]  Eric D. Dodds,et al.  Gas-phase dissociation of glycosylated peptide ions. , 2012, Mass spectrometry reviews.

[86]  J. Peter-Katalinic,et al.  Structure elucidation of glycoproteins by direct nanoESI MS and MS/MS analysis of proteolytic glycopeptides. , 2007, Journal of mass spectrometry : JMS.

[87]  T. Takao,et al.  Site-specific carbohydrate profiling of human transferrin by nano-flow liquid chromatography/electrospray ionization mass spectrometry. , 2004, Rapid communications in mass spectrometry : RCM.

[88]  Y. Mechref,et al.  Characterizing protein glycosylation sites through higher-energy C-trap dissociation. , 2010, Rapid communications in mass spectrometry : RCM.

[89]  A. J. Clifford,et al.  BIOCHIMICA ET BIOPHYSICA ACTA , 2022 .

[90]  A. Burlingame,et al.  Site-specific characterization of the N-linked glycans of murine prion protein by high-performance liquid chromatography/electrospray mass spectrometry and exoglycosidase digestions. , 1999, Biochemistry.

[91]  B. Coddeville,et al.  Comparative study of the primary structures of sero-, lacto- and ovotransferrin glycans from different species. , 1988, Biochimie.

[92]  Haixu Tang,et al.  Improving confidence in detection and characterization of protein N-glycosylation sites and microheterogeneity. , 2011, Rapid communications in mass spectrometry : RCM.

[93]  H. Brogren,et al.  Heterogeneous glycosylation patterns of human PAI-1 may reveal its cellular origin. , 2008, Thrombosis research.

[94]  André M Deelder,et al.  Protein O-glycosylation analysis , 2012, Biological chemistry.

[95]  K. Medzihradszky,et al.  Affinity Enrichment and Characterization of Mucin Core-1 Type Glycopeptides from Bovine Serum* , 2009, Molecular & Cellular Proteomics.

[96]  B. Domon,et al.  A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates , 1988, Glycoconjugate Journal.

[97]  Haixu Tang,et al.  Interlaboratory Study on Differential Analysis of Protein Glycosylation by Mass Spectrometry: The ABRF Glycoprotein Research Multi-Institutional Study 2012* , 2013, Molecular & Cellular Proteomics.

[98]  J. Olsen,et al.  Immature truncated O-glycophenotype of cancer directly induces oncogenic features , 2014, Proceedings of the National Academy of Sciences.

[99]  Robert J Chalkley,et al.  Characterizing sialic acid variants at the glycopeptide level. , 2015, Analytical chemistry.

[100]  M. Zehl,et al.  Determination of glycopeptide structures by multistage mass spectrometry with low-energy collision-induced dissociation: comparison of electrospray ionization quadrupole ion trap and matrix-assisted laser desorption/ionization quadrupole ion trap reflectron time-of-flight approaches. , 2004, Rapid communications in mass spectrometry : RCM.

[101]  R. Siciliano,et al.  Glycosylation site analysis of human alpha-1-acid glycoprotein (AGP) by capillary liquid chromatography-electrospray mass spectrometry. , 2005, Journal of mass spectrometry : JMS.

[102]  G. Larson,et al.  Molecular pathogenesis of a new glycogenosis caused by a glycogenin-1 mutation. , 2012, Biochimica et biophysica acta.

[103]  G. Larson,et al.  Sialic acid capture-and-release and LC-MS(n) analysis of glycopeptides. , 2013, Methods in molecular biology.

[104]  Adnan Halim,et al.  Advances in mass spectrometry driven O-glycoproteomics. , 2015, Biochimica et biophysica acta.

[105]  Carolyn R. Bertozzi,et al.  Essentials of Glycobiology , 1999 .

[106]  M. Raftery,et al.  Glycosylation and Sialylation of Macrophage-derived Human Apolipoprotein E Analyzed by SDS-PAGE and Mass Spectrometry , 2010, Molecular & Cellular Proteomics.