Identification of rare alternative splicing events in MS/MS data reveals a significant 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...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2014-11-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/673.pdf |
| _version_ | 1797420767569248256 |
|---|---|
| author | José E. Kroll Sandro J. de Souza Gustavo A. de Souza |
| author_facet | José E. Kroll Sandro J. de Souza Gustavo A. de Souza |
| author_sort | José E. Kroll |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T07:06:18Z |
| format | Article |
| id | doaj.art-6d306e1c5d864671a19b248125e7921d |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:06:18Z |
| publishDate | 2014-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-6d306e1c5d864671a19b248125e7921d2023-12-03T09:30:46ZengPeerJ Inc.PeerJ2167-83592014-11-012e67310.7717/peerj.673673Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sitesJosé E. Kroll0Sandro J. de Souza1Gustavo A. de Souza2Institute of Bioinformatics and Biotechnology, Natal, BrazilBrain Institute, UFRN, Natal, BrazilDepartment of Immunology and Centre for Immune Regulation, Oslo University Hospital HF Rikshospitalet, University of Oslo, Oslo, NorwayIntegration 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.https://peerj.com/articles/673.pdfMass spectrometryProteomicsAlternative splicing eventsPeptide identificationTranslation initiation sites |
| spellingShingle | José E. Kroll Sandro J. de Souza Gustavo A. de Souza Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites PeerJ Mass spectrometry Proteomics Alternative splicing events Peptide identification Translation initiation sites |
| title | Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites |
| title_full | Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites |
| title_fullStr | Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites |
| title_full_unstemmed | Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites |
| title_short | Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites |
| title_sort | identification of rare alternative splicing events in ms ms data reveals a significant fraction of alternative translation initiation sites |
| topic | Mass spectrometry Proteomics Alternative splicing events Peptide identification Translation initiation sites |
| url | https://peerj.com/articles/673.pdf |
| work_keys_str_mv | AT joseekroll identificationofrarealternativesplicingeventsinmsmsdatarevealsasignificantfractionofalternativetranslationinitiationsites AT sandrojdesouza identificationofrarealternativesplicingeventsinmsmsdatarevealsasignificantfractionofalternativetranslationinitiationsites AT gustavoadesouza identificationofrarealternativesplicingeventsinmsmsdatarevealsasignificantfractionofalternativetranslationinitiationsites |