Abstract
BackgroundDaphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the Daphnia pulex genome both open future avenues of research on this model organism. As proteomics is not only essential to our understanding of cell function, and is also a powerful validation tool for predicted genes in genome annotation projects, a first proteomic dataset is presented in this article.ResultsA comprehensive set of 701,274 peptide tandem-mass-spectra, derived from Daphnia pulex, was generated, which lead to the identification of 531 proteins. To measure the impact of the Daphnia pulex filtered models database for mass spectrometry based Daphnia protein identification, this result was compared with results obtained with the Swiss-Prot and the Drosophila melanogaster database. To further validate the utility of the Daphnia pulex database for research on other Daphnia species, additional 407,778 peptide tandem-mass-spectra, obtained from Daphnia longicephala, were generated and evaluated, leading to the identification of 317 proteins.ConclusionPeptides identified in our approach provide the first experimental evidence for the translation of a broad variety of predicted coding regions within the Daphnia genome. Furthermore it could be demonstrated that identification of Daphnia longicephala proteins using the Daphnia pulex protein database is feasible but shows a slightly reduced identification rate. Data provided in this article clearly demonstrates that the Daphnia genome database is the key for mass spectrometry based high throughput proteomics in Daphnia.
Highlights
Daphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences
Results obtained with liquid chromatography (LC)-tandem mass spectrometry (MS/mass spectrometry (MS)) Using SDS-PAGE combined with 1D-LC-MS/MS, we identified 186 entries whereas the SDS-PAGE – 2D-LC-MS combination led to the identification of 524 entries from the non-redundant filtered models database of putative Daphnia proteins demonstrating the benefit of a second chromatographic step
Considering that the main goal of our experiments was to test the benefit of a dedicated Daphnia protein database for LC-MS/MS-based proteomics, this result is promising with respect to the straightforward design of this pilot study
Summary
Commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the Daphnia pulex genome both open future avenues of research on this model organism. As proteomics is essential to our understanding of cell function, and is a powerful validation tool for predicted genes in genome annotation projects, a first proteomic dataset is presented in this article. BMC Genomics 2009, 10:171 http://www.biomedcentral.com/1471-2164/10/171 researchers in almost every field of modern biology. In addition they provide the basis for powerful technologies to quantitatively analyze the gene expression profile on the mRNA-level using DNA microarrays [1,2]. The field of high-throughput identification and quantification of proteins using systematic approaches is commonly referred to as proteomics. Large proteome investigations have been established covering, e.g., human plasma [6], human brain [7] and human liver [8] as well as model organisms such as Caenorhabditis elegans [9] and Drosophila melanogaster [10]
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