Document Detail


Database independent proteomics analysis of the ostrich and human proteome.
MedLine Citation:
PMID:  22198768     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
A F Maarten Altelaar; Danny Navarro; Jos Boekhorst; Bas van Breukelen; Berend Snel; Shabaz Mohammed; Albert J R Heck
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't     Date:  2011-12-22
Journal Detail:
Title:  Proceedings of the National Academy of Sciences of the United States of America     Volume:  109     ISSN:  1091-6490     ISO Abbreviation:  Proc. Natl. Acad. Sci. U.S.A.     Publication Date:  2012 Jan 
Date Detail:
Created Date:  2012-01-11     Completed Date:  2012-03-12     Revised Date:  2013-06-26    
Medline Journal Info:
Nlm Unique ID:  7505876     Medline TA:  Proc Natl Acad Sci U S A     Country:  United States    
Other Details:
Languages:  eng     Pagination:  407-12     Citation Subset:  IM    
Affiliation:
Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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MeSH Terms
Descriptor/Qualifier:
Animals
Cell Line
Chromatography, Ion Exchange
Chromatography, Liquid
Computational Biology
Humans
Likelihood Functions
Mass Spectrometry / methods*
Peptides / genetics*
Phylogeny*
Proteomics / methods*
Sequence Analysis, DNA / methods*
Struthioniformes / genetics*
Chemical
Reg. No./Substance:
0/Peptides
Comments/Corrections

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