That's one option. Alternatively, you can rename your proteins to have a known prefix and then use the RefreshParser tool to remap your pepXML files. You will have to rerun ProteinProphet but you won't have to redo the search. The latter option requires use of the commandline while the former requires redoing the search.
-David On Wed, May 21, 2014 at 8:28 AM, 钟传奇 <[email protected]> wrote: > Thank David for reply. > So the only way is that I have to search my data against the database with > decoy proteins tagged prefix "rev_". > > > On Wed, May 21, 2014 at 11:23 PM, David Shteynberg < > [email protected]> wrote: > >> Yes indeed...the suffix prefix distinction is very important. All top >> decoy tools expect decoys to be labeled with prefix. >> >> David >> On May 20, 2014 11:19 PM, "钟传奇" <[email protected]> wrote: >> >>> Hi, I have used Mayu integrated in TPP to analyze my data. >>> The log file of Mayu showed that there is no decoy proteins found, and >>> the log file is in the attachment. >>> I generated my database for searching with other tools than the " >>> reverse_fasta.pl" tool in the Mayu, and set the parameter "Tag (prefix) >>> for decoy proteins" as "_REVERSED". >>> I am wondering that the decoy proteins in my database fasta is >>> tagged(Suffix) "_REVERSED", has this any effect on Mayu performance? >>> >>> Any suggestion will be welcomed. >>> >>> Thanks. >>> >>> -- >>> 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. >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- >> 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. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > 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. > For more options, visit https://groups.google.com/d/optout. > -- 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. For more options, visit https://groups.google.com/d/optout.
