A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-splice...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Mo, Fan [verfasserIn] Hong, Xu Gao, Feng Du, Lin Wang, Jun Omenn, Gilbert S Lin, Biaoyang

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2008

Schlagwörter:	Alternative Splice Splice Event Alternative Splice Event Alternative Splice Variant Decoy Database

Anmerkung:	© Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (

Übergeordnetes Werk:	Enthalten in: BMC bioinformatics - London : BioMed Central, 2000, 9(2008), 1 vom: 16. Dez.
Übergeordnetes Werk:	volume:9 ; year:2008 ; number:1 ; day:16 ; month:12

Links:	Volltext

DOI / URN:	10.1186/1471-2105-9-537

Katalog-ID:	SPR026847566

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245	1	2	\|a A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
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520			\|a Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data.
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700	1		\|a Hong, Xu \|4 aut
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700	1		\|a Du, Lin \|4 aut
700	1		\|a Wang, Jun \|4 aut
700	1		\|a Omenn, Gilbert S \|4 aut
700	1		\|a Lin, Biaoyang \|4 aut
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912			\|a GBV_ILN_4335
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author_variant	f m fm x h xh f g fg l d ld j w jw g s o gs gso b l bl
matchkey_str	article:14712105:2008----::cmaileoeojntodtbsfrhietfctooeosipneet
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allfields	10.1186/1471-2105-9-537 doi (DE-627)SPR026847566 (SPR)1471-2105-9-537-e DE-627 ger DE-627 rakwb eng Mo, Fan verfasserin aut A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data. Alternative Splice (dpeaa)DE-He213 Splice Event (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Alternative Splice Variant (dpeaa)DE-He213 Decoy Database (dpeaa)DE-He213 Hong, Xu aut Gao, Feng aut Du, Lin aut Wang, Jun aut Omenn, Gilbert S aut Lin, Biaoyang aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 9(2008), 1 vom: 16. Dez. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:9 year:2008 number:1 day:16 month:12 https://dx.doi.org/10.1186/1471-2105-9-537 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 9 2008 1 16 12
spelling	10.1186/1471-2105-9-537 doi (DE-627)SPR026847566 (SPR)1471-2105-9-537-e DE-627 ger DE-627 rakwb eng Mo, Fan verfasserin aut A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data. Alternative Splice (dpeaa)DE-He213 Splice Event (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Alternative Splice Variant (dpeaa)DE-He213 Decoy Database (dpeaa)DE-He213 Hong, Xu aut Gao, Feng aut Du, Lin aut Wang, Jun aut Omenn, Gilbert S aut Lin, Biaoyang aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 9(2008), 1 vom: 16. Dez. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:9 year:2008 number:1 day:16 month:12 https://dx.doi.org/10.1186/1471-2105-9-537 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 9 2008 1 16 12
allfields_unstemmed	10.1186/1471-2105-9-537 doi (DE-627)SPR026847566 (SPR)1471-2105-9-537-e DE-627 ger DE-627 rakwb eng Mo, Fan verfasserin aut A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data. Alternative Splice (dpeaa)DE-He213 Splice Event (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Alternative Splice Variant (dpeaa)DE-He213 Decoy Database (dpeaa)DE-He213 Hong, Xu aut Gao, Feng aut Du, Lin aut Wang, Jun aut Omenn, Gilbert S aut Lin, Biaoyang aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 9(2008), 1 vom: 16. Dez. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:9 year:2008 number:1 day:16 month:12 https://dx.doi.org/10.1186/1471-2105-9-537 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 9 2008 1 16 12
allfieldsGer	10.1186/1471-2105-9-537 doi (DE-627)SPR026847566 (SPR)1471-2105-9-537-e DE-627 ger DE-627 rakwb eng Mo, Fan verfasserin aut A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data. Alternative Splice (dpeaa)DE-He213 Splice Event (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Alternative Splice Variant (dpeaa)DE-He213 Decoy Database (dpeaa)DE-He213 Hong, Xu aut Gao, Feng aut Du, Lin aut Wang, Jun aut Omenn, Gilbert S aut Lin, Biaoyang aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 9(2008), 1 vom: 16. Dez. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:9 year:2008 number:1 day:16 month:12 https://dx.doi.org/10.1186/1471-2105-9-537 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 9 2008 1 16 12
allfieldsSound	10.1186/1471-2105-9-537 doi (DE-627)SPR026847566 (SPR)1471-2105-9-537-e DE-627 ger DE-627 rakwb eng Mo, Fan verfasserin aut A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data. Alternative Splice (dpeaa)DE-He213 Splice Event (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Alternative Splice Variant (dpeaa)DE-He213 Decoy Database (dpeaa)DE-He213 Hong, Xu aut Gao, Feng aut Du, Lin aut Wang, Jun aut Omenn, Gilbert S aut Lin, Biaoyang aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 9(2008), 1 vom: 16. Dez. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:9 year:2008 number:1 day:16 month:12 https://dx.doi.org/10.1186/1471-2105-9-537 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 9 2008 1 16 12
language	English
source	Enthalten in BMC bioinformatics 9(2008), 1 vom: 16. Dez. volume:9 year:2008 number:1 day:16 month:12
sourceStr	Enthalten in BMC bioinformatics 9(2008), 1 vom: 16. Dez. volume:9 year:2008 number:1 day:16 month:12
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Alternative Splice Splice Event Alternative Splice Event Alternative Splice Variant Decoy Database
isfreeaccess_bool	true
container_title	BMC bioinformatics
authorswithroles_txt_mv	Mo, Fan @@aut@@ Hong, Xu @@aut@@ Gao, Feng @@aut@@ Du, Lin @@aut@@ Wang, Jun @@aut@@ Omenn, Gilbert S @@aut@@ Lin, Biaoyang @@aut@@
publishDateDaySort_date	2008-12-16T00:00:00Z
hierarchy_top_id	326644814
id	SPR026847566
language_de	englisch
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author	Mo, Fan
spellingShingle	Mo, Fan misc Alternative Splice misc Splice Event misc Alternative Splice Event misc Alternative Splice Variant misc Decoy Database A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
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topic_title	A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data Alternative Splice (dpeaa)DE-He213 Splice Event (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Alternative Splice Variant (dpeaa)DE-He213 Decoy Database (dpeaa)DE-He213
topic	misc Alternative Splice misc Splice Event misc Alternative Splice Event misc Alternative Splice Variant misc Decoy Database
topic_unstemmed	misc Alternative Splice misc Splice Event misc Alternative Splice Event misc Alternative Splice Variant misc Decoy Database
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title	A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
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title_full	A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
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title_sort	compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
title_auth	A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
abstract	Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data. © Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstractGer	Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data. © Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstract_unstemmed	Background Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Conclusion Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data. © Mo et al; licensee BioMed Central Ltd. 2008. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
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title_short	A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
url	https://dx.doi.org/10.1186/1471-2105-9-537
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author2	Hong, Xu Gao, Feng Du, Lin Wang, Jun Omenn, Gilbert S Lin, Biaoyang
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A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

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