Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination
Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Sobott, Frank [verfasserIn] |
|---|
| Format: |
Artikel |
|---|---|
| Sprache: |
Englisch |
| Erschienen: |
2009 |
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| Schlagwörter: |
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| Anmerkung: |
© American Society for Mass Spectrometry 2009 |
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| Übergeordnetes Werk: |
Enthalten in: Journal of the American Society for Mass Spectrometry - Springer-Verlag, 1990, 20(2009), 9 vom: Sept., Seite 1652-1659 |
|---|---|
| Übergeordnetes Werk: |
volume:20 ; year:2009 ; number:9 ; month:09 ; pages:1652-1659 |
| Links: |
|---|
| DOI / URN: |
10.1016/j.jasms.2009.04.023 |
|---|
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OLC2097684467 |
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| 520 | |a Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. | ||
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10.1016/j.jasms.2009.04.023 doi (DE-627)OLC2097684467 (DE-He213)j.jasms.2009.04.023-p DE-627 ger DE-627 rakwb eng 530 VZ 11 ssgn Sobott, Frank verfasserin aut Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination 2009 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © American Society for Mass Spectrometry 2009 Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. Collision Induce Dissociation Electron Capture Dissociation Electron Transfer Dissociation Ubiquitination Site Reagent Anion Watt, Stephen J. aut Smith, Julia aut Edelmann, Mariola J. aut Kramer, Holger B. aut Kessler, Benedikt M. aut Enthalten in Journal of the American Society for Mass Spectrometry Springer-Verlag, 1990 20(2009), 9 vom: Sept., Seite 1652-1659 (DE-627)130977357 (DE-600)1073671-2 (DE-576)277732093 1044-0305 nnns volume:20 year:2009 number:9 month:09 pages:1652-1659 https://doi.org/10.1016/j.jasms.2009.04.023 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-PHY SSG-OLC-CHE GBV_ILN_70 GBV_ILN_2004 GBV_ILN_4012 GBV_ILN_4125 GBV_ILN_4307 AR 20 2009 9 09 1652-1659 |
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10.1016/j.jasms.2009.04.023 doi (DE-627)OLC2097684467 (DE-He213)j.jasms.2009.04.023-p DE-627 ger DE-627 rakwb eng 530 VZ 11 ssgn Sobott, Frank verfasserin aut Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination 2009 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © American Society for Mass Spectrometry 2009 Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. Collision Induce Dissociation Electron Capture Dissociation Electron Transfer Dissociation Ubiquitination Site Reagent Anion Watt, Stephen J. aut Smith, Julia aut Edelmann, Mariola J. aut Kramer, Holger B. aut Kessler, Benedikt M. aut Enthalten in Journal of the American Society for Mass Spectrometry Springer-Verlag, 1990 20(2009), 9 vom: Sept., Seite 1652-1659 (DE-627)130977357 (DE-600)1073671-2 (DE-576)277732093 1044-0305 nnns volume:20 year:2009 number:9 month:09 pages:1652-1659 https://doi.org/10.1016/j.jasms.2009.04.023 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-PHY SSG-OLC-CHE GBV_ILN_70 GBV_ILN_2004 GBV_ILN_4012 GBV_ILN_4125 GBV_ILN_4307 AR 20 2009 9 09 1652-1659 |
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10.1016/j.jasms.2009.04.023 doi (DE-627)OLC2097684467 (DE-He213)j.jasms.2009.04.023-p DE-627 ger DE-627 rakwb eng 530 VZ 11 ssgn Sobott, Frank verfasserin aut Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination 2009 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © American Society for Mass Spectrometry 2009 Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. Collision Induce Dissociation Electron Capture Dissociation Electron Transfer Dissociation Ubiquitination Site Reagent Anion Watt, Stephen J. aut Smith, Julia aut Edelmann, Mariola J. aut Kramer, Holger B. aut Kessler, Benedikt M. aut Enthalten in Journal of the American Society for Mass Spectrometry Springer-Verlag, 1990 20(2009), 9 vom: Sept., Seite 1652-1659 (DE-627)130977357 (DE-600)1073671-2 (DE-576)277732093 1044-0305 nnns volume:20 year:2009 number:9 month:09 pages:1652-1659 https://doi.org/10.1016/j.jasms.2009.04.023 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-PHY SSG-OLC-CHE GBV_ILN_70 GBV_ILN_2004 GBV_ILN_4012 GBV_ILN_4125 GBV_ILN_4307 AR 20 2009 9 09 1652-1659 |
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10.1016/j.jasms.2009.04.023 doi (DE-627)OLC2097684467 (DE-He213)j.jasms.2009.04.023-p DE-627 ger DE-627 rakwb eng 530 VZ 11 ssgn Sobott, Frank verfasserin aut Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination 2009 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © American Society for Mass Spectrometry 2009 Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. Collision Induce Dissociation Electron Capture Dissociation Electron Transfer Dissociation Ubiquitination Site Reagent Anion Watt, Stephen J. aut Smith, Julia aut Edelmann, Mariola J. aut Kramer, Holger B. aut Kessler, Benedikt M. aut Enthalten in Journal of the American Society for Mass Spectrometry Springer-Verlag, 1990 20(2009), 9 vom: Sept., Seite 1652-1659 (DE-627)130977357 (DE-600)1073671-2 (DE-576)277732093 1044-0305 nnns volume:20 year:2009 number:9 month:09 pages:1652-1659 https://doi.org/10.1016/j.jasms.2009.04.023 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC SSG-OLC-PHY SSG-OLC-CHE GBV_ILN_70 GBV_ILN_2004 GBV_ILN_4012 GBV_ILN_4125 GBV_ILN_4307 AR 20 2009 9 09 1652-1659 |
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Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination |
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(DE-627)OLC2097684467 (DE-He213)j.jasms.2009.04.023-p |
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Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination |
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Sobott, Frank |
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Journal of the American Society for Mass Spectrometry |
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Sobott, Frank Watt, Stephen J. Smith, Julia Edelmann, Mariola J. Kramer, Holger B. Kessler, Benedikt M. |
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comparison of cid versus etd based ms/ms fragmentation for the analysis of protein ubiquitination |
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Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination |
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Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. © American Society for Mass Spectrometry 2009 |
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Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. © American Society for Mass Spectrometry 2009 |
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Abstract Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. © American Society for Mass Spectrometry 2009 |
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Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination |
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