Identifcation of rare alternative splicing events in MS/MS data reveals a signifcant fraction of alternative translation initiation sites

Integration of transcriptome data is a crucial step for the identification of rare protein variants in mass-spectrometry (MS) data with important consequences for all branches of biotechnology research. Here, we used Splooce, a database of splicing variants recently developed by us, to search MS dat...

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Principais autores: Kroll, José Eduardo, Souza, Sandro José de, Souza, Gustavo A. de
Formato: article
Idioma:eng
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Assuntos:
Alternative splicing events
Mass spectrometry
Peptide identification
Proteomics
Translation initiation sites
Endereço do item:https://repositorio.ufrn.br/jspui/handle/123456789/23223
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spelling ri-123456789-232232021-07-09T22:44:27Z Identifcation of rare alternative splicing events in MS/MS data reveals a signifcant fraction of alternative translation initiation sites Kroll, José Eduardo Souza, Sandro José de Souza, Gustavo A. de Alternative splicing events Mass spectrometry Peptide identification Proteomics Translation initiation sites Integration of transcriptome data is a crucial step for the identification of rare protein variants in mass-spectrometry (MS) data with important consequences for all branches of biotechnology research. Here, we used Splooce, a database of splicing variants recently developed by us, to search MS data derived from a variety of human tumor cell lines. More than 800 new protein variants were identified whose corresponding MS spectra were specific to protein entries from Splooce. Although the types of splicing variants (exon skipping, alternative splice sites and intron retention) were found at the same frequency as in the transcriptome, we observed a large variety of modifications at the protein level induced by alternative splicing events. Surprisingly, we found that 40% of all protein modifications induced by alternative splicing led to the use of alternative translation initiation sites. Other modifications include frameshifts in the open reading frame and inclusion or deletion of peptide sequences. To make the dataset generated here available to the community in a more effective form, the Splooce portal (http://www.bioinformatics-brazil.org/splooce) was modified to report the alternative splicing events supported by MS data. 2017-05-30T16:59:45Z 2017-05-30T16:59:45Z 2014-11-13 article https://repositorio.ufrn.br/jspui/handle/123456789/23223 10.7717/peerj.673 eng Acesso Aberto application/pdf
institution Repositório Institucional
collection RI - UFRN
language eng
topic Alternative splicing events
Mass spectrometry
Peptide identification
Proteomics
Translation initiation sites
spellingShingle Alternative splicing events
Mass spectrometry
Peptide identification
Proteomics
Translation initiation sites
Kroll, José Eduardo
Souza, Sandro José de
Souza, Gustavo A. de
Identifcation of rare alternative splicing events in MS/MS data reveals a signifcant fraction of alternative translation initiation sites
description Integration of transcriptome data is a crucial step for the identification of rare protein variants in mass-spectrometry (MS) data with important consequences for all branches of biotechnology research. Here, we used Splooce, a database of splicing variants recently developed by us, to search MS data derived from a variety of human tumor cell lines. More than 800 new protein variants were identified whose corresponding MS spectra were specific to protein entries from Splooce. Although the types of splicing variants (exon skipping, alternative splice sites and intron retention) were found at the same frequency as in the transcriptome, we observed a large variety of modifications at the protein level induced by alternative splicing events. Surprisingly, we found that 40% of all protein modifications induced by alternative splicing led to the use of alternative translation initiation sites. Other modifications include frameshifts in the open reading frame and inclusion or deletion of peptide sequences. To make the dataset generated here available to the community in a more effective form, the Splooce portal (http://www.bioinformatics-brazil.org/splooce) was modified to report the alternative splicing events supported by MS data.
format article
author Kroll, José Eduardo
Souza, Sandro José de
Souza, Gustavo A. de
author_facet Kroll, José Eduardo
Souza, Sandro José de
Souza, Gustavo A. de
author_sort Kroll, José Eduardo
title Identifcation of rare alternative splicing events in MS/MS data reveals a signifcant fraction of alternative translation initiation sites
title_short Identifcation of rare alternative splicing events in MS/MS data reveals a signifcant fraction of alternative translation initiation sites
title_full Identifcation of rare alternative splicing events in MS/MS data reveals a signifcant fraction of alternative translation initiation sites
title_fullStr Identifcation of rare alternative splicing events in MS/MS data reveals a signifcant fraction of alternative translation initiation sites
title_full_unstemmed Identifcation of rare alternative splicing events in MS/MS data reveals a signifcant fraction of alternative translation initiation sites
title_sort identifcation of rare alternative splicing events in ms/ms data reveals a signifcant fraction of alternative translation initiation sites
publishDate 2017
url https://repositorio.ufrn.br/jspui/handle/123456789/23223
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AT souzasandrojosede identifcationofrarealternativesplicingeventsinmsmsdatarevealsasignifcantfractionofalternativetranslationinitiationsites
AT souzagustavoade identifcationofrarealternativesplicingeventsinmsmsdatarevealsasignifcantfractionofalternativetranslationinitiationsites
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