This is a good question. In general iprophet relies on having a similar set of peptides available for matching for any given spectrum. When tandem finds a modified pep that OMSSA never even searches for it will be given a lower score by iprophet that an unmoded pep found by both engines with same criteria since the first one is found by two engines and the second by one only. However, in practice the results might not be affected very much, you can use decoys in the DB to test various ways of running iprophet. For example to reduce the effect described here you might try to run iprophet without using the multiple search engines model to not punish the mod peptids too much. This option is NONSS for iprophet.
-David Gabriel Gray <[email protected]> wrote: >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? > >-- >You received this message because you are subscribed to the Google Groups >"spctools-discuss" group. >To post to this group, send email to [email protected]. >To unsubscribe from this group, send email to >[email protected]. >For more options, visit this group at >http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
