Hi there, We recently download the TPP 6.0 RC and while using it we noticed that we obtain fewer peptides IDs than what we got for the same dataset and search output with version 5.2. Many of the missing peptides seem to have decent Expect value and MS/MS following a visual inspection. This seems that this is due to changes in PeptideProphet and are not related to the search itself that was done with Comet. Is there any additional parameter that should be included in the new version in order to restore the missing peptides? Many thanks, Oded
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