title: Database independent proteomics analysis of the ostrich and human proteome.
abstract: 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.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.
authors.forename: A F Maarten
authors.initials: AF
authors.lastname: Altelaar
authors.forename: Danny
authors.initials: D
authors.lastname: Navarro
authors.forename: Jos
authors.initials: J
authors.lastname: Boekhorst
authors.forename: Bas
authors.initials: B
authors.lastname: van Breukelen
authors.forename: Berend
authors.initials: B
authors.lastname: Snel
authors.forename: Shabaz
authors.initials: S
authors.lastname: Mohammed
authors.forename: Albert J R
authors.initials: AJ
authors.lastname: Heck
mesh_terms: D000818:Animals; D002460:Cell Line; D002852:Chromatography, Ion Exchange; D002853:Chromatography, Liquid; D019295:Computational Biology; D006801:Humans; D016013:Likelihood Functions; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000235:genetics*; D010802:Phylogeny; D040901:Proteomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020310:Struthioniformes / Q000235:genetics*
chemical_list: D010455:Peptides