Dear TPP developers, I have a question regarding how iProphet handles ambiguous I/L IDs from different search engine. I am using X!Tandem, Comet, and MSGF+ and combine the results using iProphet, and noticed that the three search engines have different rules ranking I/L hits. So how does iProphet handle such case if different search engines give different I/L variant as top ranking PSM? Does iProphet threat different I/L variant peptide as different IDs and therefore penalizing the final probability score, or iProphet considers them as the same ID?
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