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The number of accepted SSMs at a 1 % FDR threshold for various searches of the iPRG2012 data set. The open search identifies all unmodified spectra previously identified in the standard search as well as additional modified spectra. A further increase in identifications is achieved by using the shifted dot product to score modified SSMs.
| Search mode | Similarity measure | # SSMs |
|---|---|---|
| Standard search | dot product | 4141 |
| Open search | dot product | 5160 |
| Open search | shifted dot product | 6019 |
