Database independent proteomics analysis of the ostrich and human proteome.
Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search s...
| Prif Awduron: | , , , , , , |
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| Fformat: | Journal article |
| Iaith: | English |
| Cyhoeddwyd: |
2012
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| _version_ | 1826273042094882816 |
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| author | Altelaar, A Navarro, D Boekhorst, J van Breukelen, B Snel, B Mohammed, S Heck, A |
| author_facet | Altelaar, A Navarro, D Boekhorst, J van Breukelen, B Snel, B Mohammed, S Heck, A |
| author_sort | Altelaar, A |
| collection | OXFORD |
| description | Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore "database-free" approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications. |
| first_indexed | 2024-03-06T22:22:08Z |
| format | Journal article |
| id | oxford-uuid:5568936d-571f-434d-8a4b-bc905acbee88 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T22:22:08Z |
| publishDate | 2012 |
| record_format | dspace |
| spelling | oxford-uuid:5568936d-571f-434d-8a4b-bc905acbee882022-03-26T16:43:51ZDatabase independent proteomics analysis of the ostrich and human proteome.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:5568936d-571f-434d-8a4b-bc905acbee88EnglishSymplectic Elements at Oxford2012Altelaar, ANavarro, DBoekhorst, Jvan Breukelen, BSnel, BMohammed, SHeck, AMass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore "database-free" approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications. |
| spellingShingle | Altelaar, A Navarro, D Boekhorst, J van Breukelen, B Snel, B Mohammed, S Heck, A Database independent proteomics analysis of the ostrich and human proteome. |
| title | Database independent proteomics analysis of the ostrich and human proteome. |
| title_full | Database independent proteomics analysis of the ostrich and human proteome. |
| title_fullStr | Database independent proteomics analysis of the ostrich and human proteome. |
| title_full_unstemmed | Database independent proteomics analysis of the ostrich and human proteome. |
| title_short | Database independent proteomics analysis of the ostrich and human proteome. |
| title_sort | database independent proteomics analysis of the ostrich and human proteome |
| work_keys_str_mv | AT altelaara databaseindependentproteomicsanalysisoftheostrichandhumanproteome AT navarrod databaseindependentproteomicsanalysisoftheostrichandhumanproteome AT boekhorstj databaseindependentproteomicsanalysisoftheostrichandhumanproteome AT vanbreukelenb databaseindependentproteomicsanalysisoftheostrichandhumanproteome AT snelb databaseindependentproteomicsanalysisoftheostrichandhumanproteome AT mohammeds databaseindependentproteomicsanalysisoftheostrichandhumanproteome AT hecka databaseindependentproteomicsanalysisoftheostrichandhumanproteome |