Phenyx search results can only be processed with the semi-parametric modeling based on decoys. Judging from name of your database, it does have decoys in there. Now you must tell PeptideProphet to use the semi-parametric model with xinteract option -OP and the decoy tag that all your decoy proteins begin with using xinteract flag e.g. -dDECOY if all your decoys proteins begin with DECOY. You can also use option -Od to have PeptideProphet assign non-zero probabilities to the decoy hits.
-David On Mon, Nov 8, 2010 at 2:36 PM, ira cooke <[email protected]> wrote: > Hi, > > I've been struggling to run PeptideProphet on phenyx generated pepXML > files. > > The error I get from PeptideProphet is "read in no data". Full output > from the tool is as follows; > > ------------------ <BEGIN COMMANDLINE OUTPUT>----------------- > /usr/local/tpp-4-4-0/bin/xinteract -Ninteract.pep.xml -p0 -eT -l7 -D/ > var/www/ISB/data/Databases/OnMascot/SPHuman/ > sphuman_20101013_DECOY.fasta 206_pepxml.xml > > /usr/local/tpp-4-4-0/bin/xinteract (TPP v4.4 VUVUZELA rev 0, Build > 201010010955 (linux)) > > running: "/usr/local/tpp-4-4-0/bin/InteractParser 'interact.pep.xml' > '206_pepxml.xml' -D'/var/www/ISB/data/Databases/OnMascot/SPHuman/ > sphuman_20101013_DECOY.fasta' -L'7' -E'trypsin'" > file 1: 206_pepxml.xml > processed altogether 182 results > > > results written to file /var/www/ISB/data/Projects/TRegs/SP/Phenyx/ > interact.pep.shtml > > > > command completed in 3 sec > > running: "/usr/local/tpp-4-4-0/bin/PeptideProphetParser > 'interact.pep.xml' MINPROB=0" > (PHENYX) (minprob 0) > WARNING!! The discriminant function for Phenyx 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. > init with PHENYX trypsin > MS Instrument info: Manufacturer: ThermoFinnigan, Model: default, > Ionization: FIXME, Analyzer: FIXME, Detector: FIXME > > PeptideProphet (TPP v4.4 VUVUZELA rev 0, Build 201010010955 (linux)) > akel...@isb > read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > read in no data > > command "/usr/local/tpp-4-4-0/bin/PeptideProphetParser > 'interact.pep.xml' MINPROB=0" exited with non-zero exit code: 256 > QUIT - the job is incomplete > > ------------------ <END COMMANDLINE OUTPUT>----------------- > > Note that without the -eT option I get a crash (segmentation fault). > The enzyme specified inside the phenyx pepXML is > > <sample_enzyme name="Trypsin_(KR_noP)"> > </sample_enzyme> > > (to be honest I'm not sure if this means trypsin or stricttrypsin ... > but that's probably another issue as I get the error with -eS option > as well). > > Could this error be caused by a lack of raw data files? I ran the > phenyx searches on another computer and the file contains paths to raw > data on that computer. I did try fixing the paths (and copying the > raw data to a TPP accessible location) ... but that didn't work > either. > > I guess my question is what does "read in no data" mean? Does data > refer to the original spectra, or does it refer to something in the > output of InteractParser (ie interact.pep.xml). > > Any help at all on this issue would be much appreciated > > Thanks > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
