I am considering using target-decoy FDR or directly using E-value of x!tandem?
It seems that xtandem author recommend the latter. *(* *This reference describes the idea of using reversed sequences to validated large collections of protein identifications. The GPM has this method built-in as a possible method for validation.* *N.B.: We strongly recommend that you do not use this type of method for any purpose other than comparison with other search engines. The "decoy" search methods that have been developed from this manuscript are deeply flawed algorithms for determining the confidence of peptide identification assignments.* *)* However, 1. If I use E-value, I don't know which threshold should I set. Although I tried to understand E-value, I still cant know which value is suitable. At the beginning , I thought maybe I could set it as 1e-3, but I found the default E-value of blast is 10, and this paper uses 100 (http://www.ncbi.nlm.nih.gov/pubmed/18216375). So I dare not set this threshold. 2. If I choose the target-decoy strategy, I don't know which value should I use to sort the matching, could I use hyper-score? Could anyone help me? thank you very much. ps. My database is relatively large , It may affect the choice. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
