PeptideProphet is meant to process the search results of one search engine at a time. Therefor you cannot combine the result of MSGF+ and MyriMatch in a single pass. You must process the MSGF+ data through PeptideProphet and MyriMatch data through PeptideProphet separately (remember to enable Non-parametric option). To combine the result in iProphet you must use the Combine Analyses tab and provide results already processed through PeptideProphet for iProphet analysis. I would also suggest you use Minimum Probability of 0 to help iProphet make the most use of your searches.
-David On Sun, Mar 30, 2014 at 6:59 PM, <[email protected]> wrote: > No, neither you guys said work. It still report the same error. > > 在 2014年3月27日星期四UTC+8下午11时11分07秒，David Shteynberg写道： >> >> Actually it failed because it wasn't run in Semiparametric mode. Check >> the box next to use nonparametric models and try again. >> On Mar 27, 2014 7:27 AM, "Jimmy Eng" <[email protected]> wrote: >> >>> I believe that PeptideProphet failed because you told it to use a decoy >>> tag that it could not find in any of the search results. Apparently the >>> decoy tag in MSGF+ is always "XXX_" and can't be changed. So you must set >>> that as the decoy tag and make sure that same decoy tag is used in >>> MyriMatch. >>> >>> Another option is to use a self generated target-decoy database and turn >>> off the auto-decoy option in the search engines. >>> >>> >>> On Thu, Mar 27, 2014 at 2:29 AM, <[email protected]> wrote: >>> >>>> Hi, >>>> I try to combine two different search engine results using >>>> iProphet. One is myrimatch, the other is MSGF+. >>>> The decoy database search is auto conducted by each search engine. >>>> But iProphet failed, exactly PeptideProphetParser failed, when I >>>> select "Analysis Pipeline (Tandem)" -> "Analyze Peptides" in TPP 4.6.3 >>>> to combine them. >>>> The parameters for PeptideProphet and InterProphet are showed below. >>>> >>>> >>>> <https://lh6.googleusercontent.com/-aIAyfalUSIo/UzPtqmRkHoI/AAAAAAAAAAM/RcNaJf-gpcU/s1600/QQ%E5%9B%BE%E7%89%8720140327172121.jpg> >>>> >>>> >>>> <https://lh5.googleusercontent.com/-rfMJq_uvl4c/UzPt7QykkQI/AAAAAAAAAAU/DGzmgdsYqhQ/s1600/QQ%E5%9B%BE%E7%89%8720140327172230.jpg> >>>> >>>> Here is the log. >>>> >>>> running: "C:/Inetpub/tpp-bin/PeptideProphetParser >>>> "interact.pep.xml" MINPROB=0.01 DECOY=###REV###" >>>> >>>> Using Decoy Label "###REV###". >>>> (MS-GF+) >>>> WARNING!! The discriminant function for MSGFPL is not yet complete. It is >>>> presented here to help facilitate trial and discussion. Reliance on this >>>> code for publishable scientific results is not recommended. >>>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>>> which relies on a DECOY search. >>>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>>> which relies on a DECOY search. >>>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>>> which relies on a DECOY search. >>>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>>> which relies on a DECOY search. >>>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>>> which relies on a DECOY search. >>>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>>> which relies on a DECOY search. >>>> WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, >>>> which relies on a DECOY search. >>>> init with MS-GF+ trypsin >>>> two different search engines specified: MS-GF+ and MyriMatch >>>> >>>> command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" >>>> MINPROB=0.01 DECOY=###REV###" failed: Operation not permitted >>>> >>>> command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" >>>> MINPROB=0.01 DECOY=###REV###" exited with non-zero exit code: 1 >>>> QUIT - the job is incomplete >>>> >>>> >>>> Can any body tell me why this happen? Why the PeptideProphetParser >>>> failed? >>>> >>>> By the way, it didn't print error information when I try the >>>> command manually. >>>> Thanks very much! >>>> >>>> -- >>>> 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. 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