Hi, guys
I now can run iProphet to combine search result from MSGF+, X!Tandem
and Myrimatch successfully. Thanks for your help very much.
But now I face a new problem. That is, I export the pepXML file
produced by iProphet to tab-separated file using TPP's own tool, but I do
not know what each column exactly means. The tab-separated file like the
follow.
*probability spectrum iprobability ions2 peptide
protein calc_neutral_pep_mass*
* 0.0000 120817_Protea_Serum-ABPPC_1-01.00005.00005.2 0 1/32
E.EDDDDDEEGEGEEDDMD.P ###REV###sp|Q01105|SET_HUMAN 1957.5647*
I now want to calculate the FDR at PSM level and peptide level
respectively. The problem is I do not know which column I should use. And
for peptide level,
how ? Should I choose the best hit for each peptide or concern all PSMs?
Thank you~
在 2014年3月27日星期四UTC+8下午5时29分26秒，[email protected]写道：
>
> 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!
>
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