Database independent proteomics analysis of the ostrich and human proteome

作者：Altelaar A F Maarten; Navarro Danny; Boekhorst Jos; van Breukelen Bas; Snel Berend; Mohammed Shabaz^*; Heck Albert J R

来源：Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(2): 407-412.

DOI：10.1073/pnas.1108399108

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.

• 出版日期2012-1-10