Abstract 613: A Mass Spectrometric Analysis Of Embryonic Zebrafish Proteins
Zebrafish is an attractive vertebrate model organism for studies into the molecular mechanisms of cardiovascular development, pathology and pharmacology. Studies into the genetics of protein expression are largely constrained by the availability of specific antibodies. Mass spectrometry based proteomics methods have the potential to overcome these hurdles. This requires firstly an accurate characterization of proteins accessible to targeted quantitative analysis. We applied mass spectrometric proteomic methodology and statistical analysis to create profiles of proteins expressed during zebrafish embryonic development. We detected 1307 proteins from 327,906 peptide sequence identifications at 72 hpf and 120 hpf with false identification rates of less than 1% using two dimensional chromatography tandem mass spectrometry. Close to two thirds of all detected proteins were derived from hypothetical or predicted gene models or were entirely unannotated. Comparison of protein expression in embryos by two dimensional gel electrophoresis differential in gel analysis (DIGE) revealed that proteins involved in energy production and transcription/ translation were relatively more abundant at 72 hpf consistent with the faster synthesis of cellular proteins during organismal growth. Pathway analysis revealed similar expression of proteins at both stages that relate to calcium, insulin receptor, ERK/MAP kinase, vascular epithelial growth factor signaling, and WNT/b-Catenin. Similarly both stages expressed proteins of the complement and coagulation cascades, GM-CSF, PTEN, and sonic hedgehog signaling and inflammatory signals. The data are accessible in a fully searchable database (http://bioinf.itmat.upenn.edu/zebrafish) that links protein identifications to existing resources including the Zebrafish Model Organism Database. This new resource should facilitate the selection of candidate proteins for targeted quantitation and may refine systematic genetic network analysis in vertebrate development and biology. This is the first large-scale proteome analysis of embryonic zebrafish tissue to reveal previously uncharacterized proteins and detect regulated proteins with relevance for cardiovascular function and development.