Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide

Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) valu...
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Autor*in:	Pechan, Tibor [verfasserIn] Gwaltney, Steven R

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2012

Schlagwörter:	Density Functional Theory Boltzmann Distribution Amide Nitrogen Peptide Fragmentation Entropic Correction

Anmerkung:	© Pechan and Gwaltney; licensee BioMed Central Ltd. 2012

Übergeordnetes Werk:	Enthalten in: BMC bioinformatics - London : BioMed Central, 2000, 13(2012), Suppl 15 vom: 11. Sept.
Übergeordnetes Werk:	volume:13 ; year:2012 ; number:Suppl 15 ; day:11 ; month:09

Links:	Volltext

DOI / URN:	10.1186/1471-2105-13-S15-S13

Katalog-ID:	SPR026880431

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245	1	0	\|a Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
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520			\|a Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification.
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700	1		\|a Gwaltney, Steven R \|4 aut
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publishDate	2012
allfields	10.1186/1471-2105-13-S15-S13 doi (DE-627)SPR026880431 (SPR)1471-2105-13-S15-S13-e DE-627 ger DE-627 rakwb eng Pechan, Tibor verfasserin aut Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pechan and Gwaltney; licensee BioMed Central Ltd. 2012 Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification. Density Functional Theory (dpeaa)DE-He213 Boltzmann Distribution (dpeaa)DE-He213 Amide Nitrogen (dpeaa)DE-He213 Peptide Fragmentation (dpeaa)DE-He213 Entropic Correction (dpeaa)DE-He213 Gwaltney, Steven R aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 13(2012), Suppl 15 vom: 11. Sept. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:13 year:2012 number:Suppl 15 day:11 month:09 https://dx.doi.org/10.1186/1471-2105-13-S15-S13 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2012 Suppl 15 11 09
spelling	10.1186/1471-2105-13-S15-S13 doi (DE-627)SPR026880431 (SPR)1471-2105-13-S15-S13-e DE-627 ger DE-627 rakwb eng Pechan, Tibor verfasserin aut Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pechan and Gwaltney; licensee BioMed Central Ltd. 2012 Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification. Density Functional Theory (dpeaa)DE-He213 Boltzmann Distribution (dpeaa)DE-He213 Amide Nitrogen (dpeaa)DE-He213 Peptide Fragmentation (dpeaa)DE-He213 Entropic Correction (dpeaa)DE-He213 Gwaltney, Steven R aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 13(2012), Suppl 15 vom: 11. Sept. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:13 year:2012 number:Suppl 15 day:11 month:09 https://dx.doi.org/10.1186/1471-2105-13-S15-S13 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2012 Suppl 15 11 09
allfields_unstemmed	10.1186/1471-2105-13-S15-S13 doi (DE-627)SPR026880431 (SPR)1471-2105-13-S15-S13-e DE-627 ger DE-627 rakwb eng Pechan, Tibor verfasserin aut Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pechan and Gwaltney; licensee BioMed Central Ltd. 2012 Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification. Density Functional Theory (dpeaa)DE-He213 Boltzmann Distribution (dpeaa)DE-He213 Amide Nitrogen (dpeaa)DE-He213 Peptide Fragmentation (dpeaa)DE-He213 Entropic Correction (dpeaa)DE-He213 Gwaltney, Steven R aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 13(2012), Suppl 15 vom: 11. Sept. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:13 year:2012 number:Suppl 15 day:11 month:09 https://dx.doi.org/10.1186/1471-2105-13-S15-S13 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2012 Suppl 15 11 09
allfieldsGer	10.1186/1471-2105-13-S15-S13 doi (DE-627)SPR026880431 (SPR)1471-2105-13-S15-S13-e DE-627 ger DE-627 rakwb eng Pechan, Tibor verfasserin aut Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pechan and Gwaltney; licensee BioMed Central Ltd. 2012 Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification. Density Functional Theory (dpeaa)DE-He213 Boltzmann Distribution (dpeaa)DE-He213 Amide Nitrogen (dpeaa)DE-He213 Peptide Fragmentation (dpeaa)DE-He213 Entropic Correction (dpeaa)DE-He213 Gwaltney, Steven R aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 13(2012), Suppl 15 vom: 11. Sept. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:13 year:2012 number:Suppl 15 day:11 month:09 https://dx.doi.org/10.1186/1471-2105-13-S15-S13 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2012 Suppl 15 11 09
allfieldsSound	10.1186/1471-2105-13-S15-S13 doi (DE-627)SPR026880431 (SPR)1471-2105-13-S15-S13-e DE-627 ger DE-627 rakwb eng Pechan, Tibor verfasserin aut Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pechan and Gwaltney; licensee BioMed Central Ltd. 2012 Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification. Density Functional Theory (dpeaa)DE-He213 Boltzmann Distribution (dpeaa)DE-He213 Amide Nitrogen (dpeaa)DE-He213 Peptide Fragmentation (dpeaa)DE-He213 Entropic Correction (dpeaa)DE-He213 Gwaltney, Steven R aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 13(2012), Suppl 15 vom: 11. Sept. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:13 year:2012 number:Suppl 15 day:11 month:09 https://dx.doi.org/10.1186/1471-2105-13-S15-S13 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2012 Suppl 15 11 09
language	English
source	Enthalten in BMC bioinformatics 13(2012), Suppl 15 vom: 11. Sept. volume:13 year:2012 number:Suppl 15 day:11 month:09
sourceStr	Enthalten in BMC bioinformatics 13(2012), Suppl 15 vom: 11. Sept. volume:13 year:2012 number:Suppl 15 day:11 month:09
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Density Functional Theory Boltzmann Distribution Amide Nitrogen Peptide Fragmentation Entropic Correction
isfreeaccess_bool	true
container_title	BMC bioinformatics
authorswithroles_txt_mv	Pechan, Tibor @@aut@@ Gwaltney, Steven R @@aut@@
publishDateDaySort_date	2012-09-11T00:00:00Z
hierarchy_top_id	326644814
id	SPR026880431
language_de	englisch
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author	Pechan, Tibor
spellingShingle	Pechan, Tibor misc Density Functional Theory misc Boltzmann Distribution misc Amide Nitrogen misc Peptide Fragmentation misc Entropic Correction Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
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topic_title	Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide Density Functional Theory (dpeaa)DE-He213 Boltzmann Distribution (dpeaa)DE-He213 Amide Nitrogen (dpeaa)DE-He213 Peptide Fragmentation (dpeaa)DE-He213 Entropic Correction (dpeaa)DE-He213
topic	misc Density Functional Theory misc Boltzmann Distribution misc Amide Nitrogen misc Peptide Fragmentation misc Entropic Correction
topic_unstemmed	misc Density Functional Theory misc Boltzmann Distribution misc Amide Nitrogen misc Peptide Fragmentation misc Entropic Correction
topic_browse	misc Density Functional Theory misc Boltzmann Distribution misc Amide Nitrogen misc Peptide Fragmentation misc Entropic Correction
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title	Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
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title_full	Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
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author_browse	Pechan, Tibor Gwaltney, Steven R
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doi_str_mv	10.1186/1471-2105-13-S15-S13
title_sort	calculations of relative intensities of fragment ions in the msms spectra of a doubly charged penta-peptide
title_auth	Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
abstract	Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification. © Pechan and Gwaltney; licensee BioMed Central Ltd. 2012
abstractGer	Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification. © Pechan and Gwaltney; licensee BioMed Central Ltd. 2012
abstract_unstemmed	Background Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spectrum containing several different groups of ions. The mass to charge (m/z) values of these ions can be exactly calculated following simple rules based on the possible peptide fragmentation reactions. But the (relative) intensities of the particular ions cannot be simply predicted from the amino-acid sequence of the peptide. This study presents initial work towards developing a theoretical fundamental approach to ion intensity elucidation by utilizing quantum mechanical computations. Methods MSMS spectra of the doubly charged GAVLK peptide were collected on electrospray ion trap mass spectrometers using low energy modes of fragmentation. Density functional theory (DFT) calculations were performed on the population of ion precursors to determine the fragment ion intensities corresponding to a Boltzmann distribution of the protonation of nitrogens in the peptide backbone amide bonds. Results We were able to a) predict the y and b ions intensities order in concert with the experimental observation; b) predict relative intensities of y ions with errors not exceeding the experimental variation. Conclusions These results suggest that the GAVLK peptide fragmentation process in the ion trap mass spectrometer is predominantly driven by the thermodynamic stability of the precursor ions formed upon ionization of the sample. The computational approach presented in this manuscript successfully calculated ion intensities in the mass spectra of this doubly charged tryptic peptide, based solely on its amino acid sequence. As such, this work indicates a potential of incorporating quantum mechanical calculations into mass spectrometry based algorithms for molecular identification. © Pechan and Gwaltney; licensee BioMed Central Ltd. 2012
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container_issue	Suppl 15
title_short	Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
url	https://dx.doi.org/10.1186/1471-2105-13-S15-S13
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Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide

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