Sentence examples for using the decoy search from inspiring English sources
Thus, using the decoy search method of determining FDR this "near zero" FDR would be propagated to modified peptides since the reverse sequence would not produce USTags except in rare cases described above.
The E-value threshold for each search was calculated for a 1% FDR using the decoy database search according to Kall et al.[ 47].
A repeated search against a randomized decoy database (http://www.matrixscience.com/help/decoy_help.html) using the decoy.pl script and identical search parameters let to a false-positive rate of 1.2%.
Decoy searches were performed using the automated 'Decoy' search option from Mascot.
(ii) For multiple spectrum to sequence assignments and using the same parameters, the decoy search results indicate <0.1% FDR.
On the basis of these criteria, the decoy search results indicated <1% false discovery rate (FDR).
PeptideProphet and ProteinProphet (Institute for Systems Biology) probability thresholds of 95% were calculated from the decoy searches and Scaffold was used to calculate an improved 95% peptide and protein probability threshold based on the data from the two different search algorithms.
The product ion spectra were searched against the latest version of the human subset of the International Protein Index (IPI) database containing sequences in forward and reverse orientations (v3.56, Mar 09, target-decoy) using the SEQUEST search engine in Bioworks 3.3.
Proteome Discoverer was set up to perform target-decoy database search using the Mascot search engine.
We next used a decoy database search strategy [40] (using the same search criteria as the real database search) to calculate p-values for peptide identifications as this allows us to assign the probability of a false identification based on the real data from the experiment itself [40], [63], [64].
To determine the false discovery rate (FDR), the data set was searched against a sequence-reversed decoy IPI human version 3.36 database using the same search parameters.
