Table 2.
Number of proteins identified in the rat brain sample with SEQUEST and ProLuCID after DTASelect filtering
| Search Program and filter options | Forward Hits | Decoy Hits | False Positive Rate |
|---|---|---|---|
| SEQUEST_XD | 2991 | 43 | 1.44% |
| ProLuCID_XD | 3330 | 51 | 1.53% |
| ProLuCID_Z | 3345 | 41 | 1.23% |
A twelve step MudPIT dataset with 139277 spectra was searched with SEQUEST and ProLuCID respectively and DTASelect2 was used to get the final protein lists. SEQUEST_XD for SEQUEST search and XCorr and DeltaCN for DTASelect filtering; ProLuCID_XD for ProLuCID search with XCorr and DeltaCN for DTASelect2 filtering; ProLuCID_Z for ProLuCID search and Z score only for DTASelect filtering (with additional –noxc –nodcn –sp options). DTASelect2 options –p 2 –y 1 –fp 0.05 were used for all three, and additional options (–noxc –nodcn –sp) for ProLuCID_Z to use Z score only for filtering. A protein was considered identified if it has at least two peptides pass the 5% PSM (peptide-spectrum-match) false positive rate filter and each peptide has at least one tryptical terminus.