OMSSA takes considerably longer than X!Tandem to search when searching for multiple modifications (mainly due to X!Tandem's use of "refinement" mode.) Therefore, we'd like to do the modification searches using X!Tandem and leave OMSSA to just do "normal" searches (ie only 1 modification, that of oxidation on M, but no other modifications). However, will this have a significant or negligible impact on iProphet when it tries to merge the results from X!Tandem and OMSSA, since they are technically using different criteria?
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