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We were able to identify 317 proteins from the non-redundant filtered models database of putative Daphnia pulex proteins.
All MS/MS spectra were searched against the non-redundant filtered models database of Daphnia v1.1 gene builds (July, 2007) and evaluated using the PeptideProphet software.
To determine the suitability of the non-redundant filtered models database of putative Daphnia pulex proteins for the MS-based identification of proteins from other Daphnia subgenera, a Daphnia longicephala protein lysate was generated.
Using this SDS-PAGE – 2D-LC-MS/MS combination and the non-redundant filtered models database of putative Daphnia pulex proteins, we were able to identify 671 unique peptides (PeptideProphet, false discovery rate = 1%) which could be assigned to 317 Daphnia longicephala proteins (ProteinProphet, false discovery rate = 1%).
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.
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The Building Information Model is a computer model database of building design information, which may also contain information about the building's construction, management, operations, and maintenance (Howell and Batcheler, 2005).
The reaction rates can be accessed from the model database of JWS Online Cellular Systems Modeling (http://jjj.biochem.sun.ac.za/).sun.ac.za/
To further confirm the false positive ratio given by the Trans-Proteomic pipeline we generated a so-called decoy version of the Daphnia pulex filtered models database consisting of random sequences with the same average amino acid composition.
In total, we were able to identify 531 non-redundant filtered models database proteins of putative Daphnia pulex proteins.
Our cross-species analysis approach could also be extended to data from other cell lines, tissues, and human disease, which could be used to establish an animal model database instead of cMap.
By utilizing previously generated regression models, a database of spectral reflectance information, and principles of Kubelka-Munk layering, a highly accurate shade selection program was designed.
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