ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics
Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be a...
Ausführliche Beschreibung
Autor*in: |
Wong, Jason WH [verfasserIn] |
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E-Artikel |
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Sprache: |
Englisch |
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2009 |
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Anmerkung: |
© Wong et al; licensee BioMed Central Ltd. 2009 |
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Übergeordnetes Werk: |
Enthalten in: BMC bioinformatics - London : BioMed Central, 2000, 10(2009), 1 vom: 10. Aug. |
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Übergeordnetes Werk: |
volume:10 ; year:2009 ; number:1 ; day:10 ; month:08 |
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DOI / URN: |
10.1186/1471-2105-10-244 |
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Katalog-ID: |
SPR026852578 |
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100 | 1 | |a Wong, Jason WH |e verfasserin |4 aut | |
245 | 1 | 0 | |a ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics |
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520 | |a Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. | ||
650 | 4 | |a Influenza Virus |7 (dpeaa)DE-He213 | |
650 | 4 | |a Unique Peptide |7 (dpeaa)DE-He213 | |
650 | 4 | |a Exclusion List |7 (dpeaa)DE-He213 | |
650 | 4 | |a mzXML Format |7 (dpeaa)DE-He213 | |
650 | 4 | |a Peptide Fragmentation Data |7 (dpeaa)DE-He213 | |
700 | 1 | |a Schwahn, Alexander B |4 aut | |
700 | 1 | |a Downard, Kevin M |4 aut | |
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10.1186/1471-2105-10-244 doi (DE-627)SPR026852578 (SPR)1471-2105-10-244-e DE-627 ger DE-627 rakwb eng Wong, Jason WH verfasserin aut ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wong et al; licensee BioMed Central Ltd. 2009 Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. Influenza Virus (dpeaa)DE-He213 Unique Peptide (dpeaa)DE-He213 Exclusion List (dpeaa)DE-He213 mzXML Format (dpeaa)DE-He213 Peptide Fragmentation Data (dpeaa)DE-He213 Schwahn, Alexander B aut Downard, Kevin M aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 10(2009), 1 vom: 10. Aug. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:10 year:2009 number:1 day:10 month:08 https://dx.doi.org/10.1186/1471-2105-10-244 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 10 2009 1 10 08 |
spelling |
10.1186/1471-2105-10-244 doi (DE-627)SPR026852578 (SPR)1471-2105-10-244-e DE-627 ger DE-627 rakwb eng Wong, Jason WH verfasserin aut ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wong et al; licensee BioMed Central Ltd. 2009 Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. Influenza Virus (dpeaa)DE-He213 Unique Peptide (dpeaa)DE-He213 Exclusion List (dpeaa)DE-He213 mzXML Format (dpeaa)DE-He213 Peptide Fragmentation Data (dpeaa)DE-He213 Schwahn, Alexander B aut Downard, Kevin M aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 10(2009), 1 vom: 10. Aug. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:10 year:2009 number:1 day:10 month:08 https://dx.doi.org/10.1186/1471-2105-10-244 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 10 2009 1 10 08 |
allfields_unstemmed |
10.1186/1471-2105-10-244 doi (DE-627)SPR026852578 (SPR)1471-2105-10-244-e DE-627 ger DE-627 rakwb eng Wong, Jason WH verfasserin aut ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wong et al; licensee BioMed Central Ltd. 2009 Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. Influenza Virus (dpeaa)DE-He213 Unique Peptide (dpeaa)DE-He213 Exclusion List (dpeaa)DE-He213 mzXML Format (dpeaa)DE-He213 Peptide Fragmentation Data (dpeaa)DE-He213 Schwahn, Alexander B aut Downard, Kevin M aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 10(2009), 1 vom: 10. Aug. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:10 year:2009 number:1 day:10 month:08 https://dx.doi.org/10.1186/1471-2105-10-244 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 10 2009 1 10 08 |
allfieldsGer |
10.1186/1471-2105-10-244 doi (DE-627)SPR026852578 (SPR)1471-2105-10-244-e DE-627 ger DE-627 rakwb eng Wong, Jason WH verfasserin aut ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wong et al; licensee BioMed Central Ltd. 2009 Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. Influenza Virus (dpeaa)DE-He213 Unique Peptide (dpeaa)DE-He213 Exclusion List (dpeaa)DE-He213 mzXML Format (dpeaa)DE-He213 Peptide Fragmentation Data (dpeaa)DE-He213 Schwahn, Alexander B aut Downard, Kevin M aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 10(2009), 1 vom: 10. Aug. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:10 year:2009 number:1 day:10 month:08 https://dx.doi.org/10.1186/1471-2105-10-244 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 10 2009 1 10 08 |
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10.1186/1471-2105-10-244 doi (DE-627)SPR026852578 (SPR)1471-2105-10-244-e DE-627 ger DE-627 rakwb eng Wong, Jason WH verfasserin aut ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wong et al; licensee BioMed Central Ltd. 2009 Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. Influenza Virus (dpeaa)DE-He213 Unique Peptide (dpeaa)DE-He213 Exclusion List (dpeaa)DE-He213 mzXML Format (dpeaa)DE-He213 Peptide Fragmentation Data (dpeaa)DE-He213 Schwahn, Alexander B aut Downard, Kevin M aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 10(2009), 1 vom: 10. Aug. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:10 year:2009 number:1 day:10 month:08 https://dx.doi.org/10.1186/1471-2105-10-244 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 10 2009 1 10 08 |
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ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics |
abstract |
Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. © Wong et al; licensee BioMed Central Ltd. 2009 |
abstractGer |
Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. © Wong et al; licensee BioMed Central Ltd. 2009 |
abstract_unstemmed |
Background Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or $ MS^{E} $) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. Results An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data. Conclusion The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories. © Wong et al; licensee BioMed Central Ltd. 2009 |
collection_details |
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container_issue |
1 |
title_short |
ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics |
url |
https://dx.doi.org/10.1186/1471-2105-10-244 |
remote_bool |
true |
author2 |
Schwahn, Alexander B Downard, Kevin M |
author2Str |
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hochschulschrift_bool |
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doi_str |
10.1186/1471-2105-10-244 |
up_date |
2024-07-03T23:05:33.690Z |
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