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It was also split into two, as described above for the "forward" database.
The sequences of all the URFs for the forward database were uploaded into the BLAST2GO software suite [ 22, 23].
This forward database was followed by a decoy component, which included all target protein sequences in reversed order.
Data were further processed to remove peptide spectral matches to the forward database with an FDR greater than 1.0%.
When applying that score cut-off to the peptides obtained from the forward database, 1249 of 23,376 unique peptides (5.34%) from that database were "decoy" filtered.
FPR was calculated as follows: 2xFP/ FP+TP) where FP is the number of proteins matching the reverse database and TP is the number proteins matching the forward database.
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This merged file was then re-searched in Mascot against a forward-only database.
The same concatenated forward-random database, as well as the same.mgf files generated from extract_msn was used.
The "false discovery rate (FDR)" was estimated by searching a combined forward-reversed database as described by Elias [ 35].
In an effort to further enhance the CCTR's coverage we have forwarded the database from this study to the Cochrane Collaboration's CAM field so that the information can be added to the CCTR.
If the formal group goes forward with the database effort early next year, Mr. Redenbaugh said, it will probably contract with an outside technology firm to handle that responsibility.
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