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GlyCosmos600-Glycan-Motif-Structure

{"project":"GlyCosmos600-Glycan-Motif-Structure","denotations":[{"id":"T1","span":{"begin":89,"end":97},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T2","span":{"begin":89,"end":97},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T3","span":{"begin":225,"end":244},"obj":"https://glytoucan.org/Structures/Glycans/G64581RP"},{"id":"T4","span":{"begin":246,"end":254},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T5","span":{"begin":246,"end":254},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T6","span":{"begin":531,"end":539},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T7","span":{"begin":531,"end":539},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T8","span":{"begin":721,"end":729},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T9","span":{"begin":721,"end":729},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T10","span":{"begin":826,"end":834},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T11","span":{"begin":826,"end":834},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T12","span":{"begin":1025,"end":1033},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T13","span":{"begin":1025,"end":1033},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T14","span":{"begin":1179,"end":1187},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T15","span":{"begin":1179,"end":1187},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T16","span":{"begin":1467,"end":1475},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T17","span":{"begin":1467,"end":1475},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos600-CLO

{"project":"GlyCosmos600-CLO","denotations":[{"id":"T1","span":{"begin":880,"end":885},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos6-Glycan-Motif-Image

sentences

{"project":"sentences","denotations":[{"id":"TextSentencer_T1","span":{"begin":0,"end":127},"obj":"Sentence"},{"id":"TextSentencer_T2","span":{"begin":128,"end":369},"obj":"Sentence"},{"id":"TextSentencer_T3","span":{"begin":370,"end":670},"obj":"Sentence"},{"id":"TextSentencer_T4","span":{"begin":671,"end":995},"obj":"Sentence"},{"id":"TextSentencer_T5","span":{"begin":996,"end":1206},"obj":"Sentence"},{"id":"TextSentencer_T6","span":{"begin":1207,"end":1420},"obj":"Sentence"},{"id":"TextSentencer_T7","span":{"begin":1421,"end":1655},"obj":"Sentence"},{"id":"T1","span":{"begin":0,"end":127},"obj":"Sentence"},{"id":"T2","span":{"begin":128,"end":369},"obj":"Sentence"},{"id":"T3","span":{"begin":370,"end":670},"obj":"Sentence"},{"id":"T4","span":{"begin":671,"end":995},"obj":"Sentence"},{"id":"T5","span":{"begin":996,"end":1206},"obj":"Sentence"},{"id":"T6","span":{"begin":1207,"end":1420},"obj":"Sentence"},{"id":"T7","span":{"begin":1421,"end":1655},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos6-Glycan-Motif-Structure

{"project":"GlyCosmos6-Glycan-Motif-Structure","denotations":[{"id":"T1","span":{"begin":89,"end":97},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T2","span":{"begin":89,"end":97},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T3","span":{"begin":225,"end":244},"obj":"https://glytoucan.org/Structures/Glycans/G64581RP"},{"id":"T4","span":{"begin":246,"end":254},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T5","span":{"begin":246,"end":254},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T6","span":{"begin":531,"end":539},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T7","span":{"begin":531,"end":539},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T8","span":{"begin":721,"end":729},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T9","span":{"begin":721,"end":729},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T10","span":{"begin":826,"end":834},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T11","span":{"begin":826,"end":834},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T12","span":{"begin":1025,"end":1033},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T13","span":{"begin":1025,"end":1033},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T14","span":{"begin":1179,"end":1187},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T15","span":{"begin":1179,"end":1187},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"},{"id":"T16","span":{"begin":1467,"end":1475},"obj":"https://glytoucan.org/Structures/Glycans/G49108TO"},{"id":"T17","span":{"begin":1467,"end":1475},"obj":"https://glytoucan.org/Structures/Glycans/G89565QL"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

Glycosmos6-GlycoEpitope

{"project":"Glycosmos6-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":89,"end":97},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"T2","span":{"begin":246,"end":254},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"T3","span":{"begin":531,"end":539},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"T4","span":{"begin":721,"end":729},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"T5","span":{"begin":826,"end":834},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"T6","span":{"begin":1025,"end":1033},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"T7","span":{"begin":1179,"end":1187},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"T8","span":{"begin":1467,"end":1475},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

Allie

{"project":"Allie","denotations":[{"id":"SS1_21740066_1_0","span":{"begin":214,"end":244},"obj":"expanded"},{"id":"SS2_21740066_1_0","span":{"begin":246,"end":254},"obj":"abbr"},{"id":"SS1_21740066_2_0","span":{"begin":422,"end":453},"obj":"expanded"},{"id":"SS2_21740066_2_0","span":{"begin":455,"end":458},"obj":"abbr"},{"id":"SS1_21740066_2_1","span":{"begin":464,"end":494},"obj":"expanded"},{"id":"SS2_21740066_2_1","span":{"begin":496,"end":499},"obj":"abbr"}],"relations":[{"id":"AE1_21740066_1_0","pred":"abbreviatedTo","subj":"SS1_21740066_1_0","obj":"SS2_21740066_1_0"},{"id":"AE1_21740066_2_0","pred":"abbreviatedTo","subj":"SS1_21740066_2_0","obj":"SS2_21740066_2_0"},{"id":"AE1_21740066_2_1","pred":"abbreviatedTo","subj":"SS1_21740066_2_1","obj":"SS2_21740066_2_1"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos600-GlycoEpitope

{"project":"GlyCosmos600-GlycoEpitope","denotations":[{"id":"PD-GlycoEpitope-B_T1","span":{"begin":89,"end":97},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"PD-GlycoEpitope-B_T2","span":{"begin":246,"end":254},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"PD-GlycoEpitope-B_T3","span":{"begin":531,"end":539},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"PD-GlycoEpitope-B_T4","span":{"begin":721,"end":729},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"PD-GlycoEpitope-B_T5","span":{"begin":826,"end":834},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"PD-GlycoEpitope-B_T6","span":{"begin":1025,"end":1033},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"PD-GlycoEpitope-B_T7","span":{"begin":1179,"end":1187},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"PD-GlycoEpitope-B_T8","span":{"begin":1467,"end":1475},"obj":"http://www.glycoepitope.jp/epitopes/EP0004"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos600-FMA

{"project":"GlyCosmos600-FMA","denotations":[{"id":"T1","span":{"begin":81,"end":88},"obj":"Body_part"},{"id":"T2","span":{"begin":163,"end":171},"obj":"Body_part"},{"id":"T3","span":{"begin":225,"end":244},"obj":"Body_part"},{"id":"T4","span":{"begin":496,"end":499},"obj":"Body_part"},{"id":"T5","span":{"begin":576,"end":586},"obj":"Body_part"},{"id":"T6","span":{"begin":739,"end":742},"obj":"Body_part"},{"id":"T7","span":{"begin":796,"end":799},"obj":"Body_part"},{"id":"T8","span":{"begin":844,"end":852},"obj":"Body_part"},{"id":"T9","span":{"begin":880,"end":885},"obj":"Body_part"},{"id":"T10","span":{"begin":946,"end":949},"obj":"Body_part"},{"id":"T11","span":{"begin":1105,"end":1108},"obj":"Body_part"},{"id":"T12","span":{"begin":1231,"end":1234},"obj":"Body_part"},{"id":"T13","span":{"begin":1388,"end":1396},"obj":"Body_part"},{"id":"T14","span":{"begin":1563,"end":1573},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma82787"},{"id":"A4","pred":"fma_id","subj":"T4","obj":"http://purl.org/sig/ont/fma/fma67781"},{"id":"A5","pred":"fma_id","subj":"T5","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A6","pred":"fma_id","subj":"T6","obj":"http://purl.org/sig/ont/fma/fma62872"},{"id":"A7","pred":"fma_id","subj":"T7","obj":"http://purl.org/sig/ont/fma/fma67781"},{"id":"A8","pred":"fma_id","subj":"T8","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma67781"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma67781"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma67781"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos600-GlycoGenes2

{"project":"GlyCosmos600-GlycoGenes2","denotations":[{"id":"T1","span":{"begin":89,"end":97},"obj":"https://acgg.asia/db/ggdb/info/gg114"},{"id":"T2","span":{"begin":246,"end":254},"obj":"https://acgg.asia/db/ggdb/info/gg114"},{"id":"T3","span":{"begin":531,"end":539},"obj":"https://acgg.asia/db/ggdb/info/gg114"},{"id":"T4","span":{"begin":721,"end":729},"obj":"https://acgg.asia/db/ggdb/info/gg114"},{"id":"T5","span":{"begin":826,"end":834},"obj":"https://acgg.asia/db/ggdb/info/gg114"},{"id":"T6","span":{"begin":1025,"end":1033},"obj":"https://acgg.asia/db/ggdb/info/gg114"},{"id":"T7","span":{"begin":1179,"end":1187},"obj":"https://acgg.asia/db/ggdb/info/gg114"},{"id":"T8","span":{"begin":1467,"end":1475},"obj":"https://acgg.asia/db/ggdb/info/gg114"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

NGLY1-deficiency

{"project":"NGLY1-deficiency","denotations":[{"id":"PD-NGLY1-deficiency-B_T1","span":{"begin":91,"end":97},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T2","span":{"begin":225,"end":244},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T3","span":{"begin":248,"end":254},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T4","span":{"begin":533,"end":539},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T5","span":{"begin":626,"end":632},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T6","span":{"begin":723,"end":729},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T7","span":{"begin":828,"end":834},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T8","span":{"begin":1027,"end":1033},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T9","span":{"begin":1181,"end":1187},"obj":"chem:24139"},{"id":"PD-NGLY1-deficiency-B_T10","span":{"begin":1469,"end":1475},"obj":"chem:24139"}],"namespaces":[{"prefix":"hgnc","uri":"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:"},{"prefix":"omim","uri":"https://www.omim.org/entry/"},{"prefix":"chem","uri":"https://pubchem.ncbi.nlm.nih.gov/compound/"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

pubmed-enju-pas

GlyCosmos15-Glycan

{"project":"GlyCosmos15-Glycan","denotations":[{"id":"T1","span":{"begin":89,"end":97},"obj":"Glycan"},{"id":"T2","span":{"begin":246,"end":254},"obj":"Glycan"},{"id":"T3","span":{"begin":531,"end":539},"obj":"Glycan"},{"id":"T4","span":{"begin":721,"end":729},"obj":"Glycan"},{"id":"T5","span":{"begin":826,"end":834},"obj":"Glycan"},{"id":"T6","span":{"begin":1025,"end":1033},"obj":"Glycan"},{"id":"T7","span":{"begin":1179,"end":1187},"obj":"Glycan"},{"id":"T8","span":{"begin":1467,"end":1475},"obj":"Glycan"}],"attributes":[{"id":"A1","pred":"glycosmos_id","subj":"T1","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A9","pred":"image","subj":"T1","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A2","pred":"glycosmos_id","subj":"T2","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A10","pred":"image","subj":"T2","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A3","pred":"glycosmos_id","subj":"T3","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A11","pred":"image","subj":"T3","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A4","pred":"glycosmos_id","subj":"T4","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A12","pred":"image","subj":"T4","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A5","pred":"glycosmos_id","subj":"T5","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A13","pred":"image","subj":"T5","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A6","pred":"glycosmos_id","subj":"T6","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A14","pred":"image","subj":"T6","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A7","pred":"glycosmos_id","subj":"T7","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A15","pred":"image","subj":"T7","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A8","pred":"glycosmos_id","subj":"T8","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A16","pred":"image","subj":"T8","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

Glycan-GlyCosmos

{"project":"Glycan-GlyCosmos","denotations":[{"id":"T1","span":{"begin":89,"end":97},"obj":"Glycan"},{"id":"T2","span":{"begin":246,"end":254},"obj":"Glycan"},{"id":"T3","span":{"begin":531,"end":539},"obj":"Glycan"},{"id":"T4","span":{"begin":721,"end":729},"obj":"Glycan"},{"id":"T5","span":{"begin":826,"end":834},"obj":"Glycan"},{"id":"T6","span":{"begin":1025,"end":1033},"obj":"Glycan"},{"id":"T7","span":{"begin":1179,"end":1187},"obj":"Glycan"},{"id":"T8","span":{"begin":1467,"end":1475},"obj":"Glycan"}],"attributes":[{"id":"A1","pred":"glycosmos_id","subj":"T1","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A9","pred":"image","subj":"T1","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A2","pred":"glycosmos_id","subj":"T2","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A10","pred":"image","subj":"T2","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A3","pred":"glycosmos_id","subj":"T3","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A11","pred":"image","subj":"T3","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A4","pred":"glycosmos_id","subj":"T4","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A12","pred":"image","subj":"T4","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A5","pred":"glycosmos_id","subj":"T5","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A13","pred":"image","subj":"T5","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A6","pred":"glycosmos_id","subj":"T6","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A14","pred":"image","subj":"T6","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A7","pred":"glycosmos_id","subj":"T7","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A15","pred":"image","subj":"T7","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"},{"id":"A8","pred":"glycosmos_id","subj":"T8","obj":"https://glycosmos.org/glycans/show/G49108TO"},{"id":"A16","pred":"image","subj":"T8","obj":"https://api.glycosmos.org/wurcs2image/latest/png/binary/G49108TO"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos-GlycoEpitope

{"project":"GlyCosmos-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":89,"end":97},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T2","span":{"begin":246,"end":254},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T3","span":{"begin":531,"end":539},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T4","span":{"begin":721,"end":729},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T5","span":{"begin":826,"end":834},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T6","span":{"begin":1025,"end":1033},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T7","span":{"begin":1179,"end":1187},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T8","span":{"begin":1467,"end":1475},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"}],"attributes":[{"id":"A1","pred":"glycoepitope_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A2","pred":"glycoepitope_id","subj":"T2","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A3","pred":"glycoepitope_id","subj":"T3","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A4","pred":"glycoepitope_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A5","pred":"glycoepitope_id","subj":"T5","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A6","pred":"glycoepitope_id","subj":"T6","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A7","pred":"glycoepitope_id","subj":"T7","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A8","pred":"glycoepitope_id","subj":"T8","obj":"http://www.glycoepitope.jp/epitopes/EP0004"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos15-GlycoEpitope

{"project":"GlyCosmos15-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":89,"end":97},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T2","span":{"begin":246,"end":254},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T3","span":{"begin":531,"end":539},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T4","span":{"begin":721,"end":729},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T5","span":{"begin":826,"end":834},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T6","span":{"begin":1025,"end":1033},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T7","span":{"begin":1179,"end":1187},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"},{"id":"T8","span":{"begin":1467,"end":1475},"obj":"http://purl.jp/bio/12/glyco/glycan#Glycan_epitope"}],"attributes":[{"id":"A1","pred":"glycoepitope_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A2","pred":"glycoepitope_id","subj":"T2","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A3","pred":"glycoepitope_id","subj":"T3","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A4","pred":"glycoepitope_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A5","pred":"glycoepitope_id","subj":"T5","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A6","pred":"glycoepitope_id","subj":"T6","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A7","pred":"glycoepitope_id","subj":"T7","obj":"http://www.glycoepitope.jp/epitopes/EP0004"},{"id":"A8","pred":"glycoepitope_id","subj":"T8","obj":"http://www.glycoepitope.jp/epitopes/EP0004"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}

GlyCosmos15-Sentences

{"project":"GlyCosmos15-Sentences","blocks":[{"id":"T1","span":{"begin":0,"end":127},"obj":"Sentence"},{"id":"T2","span":{"begin":128,"end":369},"obj":"Sentence"},{"id":"T3","span":{"begin":370,"end":670},"obj":"Sentence"},{"id":"T4","span":{"begin":671,"end":995},"obj":"Sentence"},{"id":"T5","span":{"begin":996,"end":1206},"obj":"Sentence"},{"id":"T6","span":{"begin":1207,"end":1420},"obj":"Sentence"},{"id":"T7","span":{"begin":1421,"end":1655},"obj":"Sentence"}],"text":"Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.\nMass spectrometry-based studies of proteins that are post-translationally modified by O-linked β-N-acetylglucosamine (O-GlcNAc) are challenged in effectively identifying the sites of modification while simultaneously sequencing the peptides. Here we tested the hypothesis that a combination of high-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) could specifically target the O-GlcNAc modified peptides and elucidate the amino acid sequence while preserving the attached GlcNAc residue for accurate site assignment. By taking advantage of the recently characterized O-GlcNAc-specific IgG monoclonal antibodies and the combination of HCD and ETD fragmentation techniques, O-GlcNAc modified proteins were enriched from HEK293T cells and subsequently characterized using the LTQ Orbitrap Velos ETD (Thermo Fisher Scientific) mass spectrometer. In our data set, 83 sites of O-GlcNAc modification are reported with high confidence confirming that the HCD/ETD combined approach is amenable to the detection and site assignment of O-GlcNAc modified peptides. Realizing HCD triggered ETD fragmentation on a linear ion trap/Orbitrap platform for more in-depth analysis and application of this technique to other post-translationally modified proteins are currently underway. Furthermore, this report illustrates that the O-GlcNAc transferase appears to demonstrate promiscuity with regards to the hydroxyl-containing amino acid modified in short stretches of primary sequence of the glycosylated polypeptides."}