Exercise MSMS2: Answers

1. Optimise the search parameters. How many peptide matches can you get at 1% false discovery rate

   Approximately 670 matches at 1% FDR (will depend on database size)

2. Change the taxonomy filter or database to green plants. What happens to the FDR? Why do you think this is?

   The FDR jumps to a very high value because the search parameters are incorrect, preventing matches in the target database. A fixed modification on the peptide N-terminus or an incorrect enzyme or a mass tolerance that is far too tight would have a similar effect. In the limit, if you cannot get matches in the target, the FDR must increase to 100%

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