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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 171.
Published online Apr 21, 2009. doi:  10.1186/1471-2164-10-171
PMCID: PMC2674882
LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia
Thomas Fröhlich,#1 Georg J Arnold,corresponding author1 Rainer Fritsch,2 Tobias Mayr,2 and Christian Laforschcorresponding author#2
1Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilian University, 81377 Munich, Germany
2Department of Biology II and GeoBio-Center, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
corresponding authorCorresponding author.
#Contributed equally.
Thomas Fröhlich: frohlich/at/lmb.uni-muenchen.de; Georg J Arnold: arnold/at/lmb.uni-muenchen.de; Rainer Fritsch: fritsch/at/zi.biologie.uni-muenchen.de; Tobias Mayr: mayr/at/zi.biologie.uni-muenchen.de; Christian Laforsch: laforsch/at/bio.lmu.de
Received March 14, 2008; Accepted April 21, 2009.
Abstract
Background
Daphniids, 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.
Results
A 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.
Conclusion
Peptides 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.
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