David, Joseph, Awesome everything works now with version 4.8.0
Thank you! Jesse On Friday, July 24, 2015 at 2:33:05 PM UTC-7, David Shteynberg wrote: > > Hello Jesse, > > > I think the issue is that ProteinProphet may not be finding the database > used in the search. Can you run RefreshParser on the commandline as > follows: > > RefreshParser > c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Kac.GluC.all.interact.pep.xml > c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Ecoli.fasta > > Then try to rerun ProteinProphet on the commandline > > ProteinProphet > c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Kac.GluC.all.interact.pep.xml > c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Kac.GluC.all.interact.prot.xml > XML > > > Let me know if you see any errors. > > Thank you, > -David > > On Fri, Jul 24, 2015 at 2:19 PM, Joseph Slagel < > [email protected] <javascript:>> wrote: > >> Jesse, >> >> Yes, I think David pinpointed an issue. It appears as if you downloaded >> a developer alpha build of TPP. As an alpha build, its expected to have >> lots of problems as it gets tested and they get fixed. I'd recommend >> downloading the latest stable TPP release, 4.8.0, from sourceforge, >> http://sourceforge.net/projects/sashimi/files/latest/download?source=files >> >> -Joe >> >> >> On Fri, Jul 24, 2015 at 2:11 PM, David Shteynberg < >> [email protected] <javascript:>> wrote: >> >>> Hi Jesse, >>> >>> This issue seems unrelated to the issue that I just corrected in >>> InteractParser. >>> >>> It appears that on your system everything is installed to C:\TPP\bin >>> whereas it should install to C:\Inetpub\tpp-bin. Are you perhaps Which >>> version are you installing? Can you try this command in the commandline to >>> see if it gives you any additional messages? >>> >>> Thank you, >>> >>> -David >>> >>> On Fri, Jul 24, 2015 at 1:15 PM, Jesse <[email protected] <javascript:>> >>> wrote: >>> >>>> Hi David, >>>> >>>> Now I'm almost certain there is a problem with the installation on my >>>> new systems. TPP wont even convert RAW files or download spectral >>>> libraries. Any suggestions about where to start? >>>> >>>> *EXECUTING: C:/TPP/bin/msconvert >>>> c:/Inetpub/wwwroot/ISB/data/dbase/OR20080317_S_SILAC-LH_1-1_01.RAW -v >>>> --mzXML -o c:/Inetpub/wwwroot/ISB/data/dbase --filter "peakPicking true >>>> [1,2]" * >>>> >>>> *Command FAILED* >>>> RETURN CODE:13568 >>>> >>>> Best, >>>> Jesse >>>> >>>> On Thursday, July 23, 2015 at 2:01:02 PM UTC-7, Jesse wrote: >>>>> >>>>> Hi David, >>>>> >>>>> I just sent you a link to the files with my new email address. I >>>>> tried without the pI model and I got the same error. I suspect a problem >>>>> with the network settings on the computers at work. >>>>> >>>>> Thanks for looking into this for me. >>>>> >>>>> Best, >>>>> Jesse >>>>> ------------------------------ >>>>> *From:* [email protected] <javascript:> [ >>>>> [email protected] <javascript:>] on behalf of David >>>>> Shteynberg [[email protected] <javascript:>] >>>>> >>>>> *Sent:* Thursday, July 23, 2015 11:58 AM >>>>> *To:* spctools-discuss >>>>> *Subject:* Re: [spctools-discuss] Re: Processing MSGF+ searches >>>>> >>>>> Hello Jesse, >>>>> >>>>> >>>>> I am not sure that I can pinpoint the error without access to your >>>>> file. Is this possible? Otherwise you can try the analysis with the >>>>> following PeptideProphetParser options removing PI model which has not >>>>> been >>>>> extensively tested through MSGF+ and could be the culprit. >>>>> >>>>> PeptideProphetParser >>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.0 >>>>> CLEVEL=2.5 >>>>> PPM DECOYPROBS ACCMASS NONTT NONPARAM DECOY=XXX_ IGNORECHG=1 >>>>> >>>>> If this works then the problem is with the pI model. >>>>> >>>>> Let me know if you can forward me your test.interact.pep.xml file to >>>>> test with. >>>>> >>>>> Thank you, >>>>> -David >>>>> >>>>> On Wed, Jul 22, 2015 at 7:57 PM, Jesse <[email protected] <javascript:>> >>>>> wrote: >>>>> >>>>>> Hi David, >>>>>> >>>>>> I'm having problems recently running PeptideProphet on MSGF+ search >>>>>> output of GluC digests. I tried the perl script you suggest but I'm not >>>>>> sure if it does anything because I'm not sure what it is supposed to do. >>>>>> >>>>>> That line is meant to replace a single "\" with "-", correct? It seems >>>>>> to >>>>>> start OK but then it quits. The GUI then prints return code: 65280. If >>>>>> you could make a quick suggestion as to whether you think the problem is >>>>>> my >>>>>> pep.xml files again or my install I would greatly appreciate it. I >>>>>> tried >>>>>> both the development release and 4.8. >>>>>> >>>>>> C:/TPP/bin/xinteract (TPP v5.0.0a2 Development, Build xxxx-xxxx >>>>>> (x86_64)) >>>>>> PPM mode in Accurate Mass Model ... >>>>>> PPM mode in Accurate Mass Model ... >>>>>> >>>>>> running: "C:/TPP/bin/InteractParser >>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" >>>>>> "150624_0002_CR1_GluC_Xyl_0p4_rep1b.pep.XML" >>>>>> "150624_0003_CR1_GluC_Xyl_4_rep1.pep.XML" >>>>>> "150624_0004_CR1_GluC_Glc_0p4_rep1.pep.XML" >>>>>> "150624_0005_CR1_GluC_Glc_4_rep1.pep.XML" >>>>>> "150624_0007_CR1_GluC_Xyl_0p4_rep2.pep.XML" >>>>>> "150624_0008_CR1_GluC_Xyl_4_rep2.pep.XML" >>>>>> "150624_0009_CR1_GluC_Glc_0p4_rep2.pep.XML" >>>>>> "150624_0010_CR1_GluC_Glc_4_rep2.pep.XML" >>>>>> "150624_0012_CR1_GluC_Xyl_0p4_rep3.pep.XML" >>>>>> "150624_0014_CR1_GluC_Xyl_4_rep3.pep.XML" >>>>>> "150624_0015_CR1_GluC_Glc_0p4_rep3.pep.XML" >>>>>> "150624_0016_CR1_GluC_Glc_4_rep3.pep.XML" -L"7" -E"nonspecific"" >>>>>> file 1: 150624_0002_CR1_GluC_Xyl_0p4_rep1b.pep.XMLWARNING: empty >>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0002_CR1_GluC_Xyl_0p4_rep1b.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 2: 150624_0003_CR1_GluC_Xyl_4_rep1.pep.XMLWARNING: empty raw_data >>>>>> in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0003_CR1_GluC_Xyl_4_rep1.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 3: 150624_0004_CR1_GluC_Glc_0p4_rep1.pep.XMLWARNING: empty >>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0004_CR1_GluC_Glc_0p4_rep1.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 4: 150624_0005_CR1_GluC_Glc_4_rep1.pep.XMLWARNING: empty raw_data >>>>>> in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0005_CR1_GluC_Glc_4_rep1.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 5: 150624_0007_CR1_GluC_Xyl_0p4_rep2.pep.XMLWARNING: empty >>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0007_CR1_GluC_Xyl_0p4_rep2.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 6: 150624_0008_CR1_GluC_Xyl_4_rep2.pep.XMLWARNING: empty raw_data >>>>>> in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0008_CR1_GluC_Xyl_4_rep2.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 7: 150624_0009_CR1_GluC_Glc_0p4_rep2.pep.XMLWARNING: empty >>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0009_CR1_GluC_Glc_0p4_rep2.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 8: 150624_0010_CR1_GluC_Glc_4_rep2.pep.XMLWARNING: empty raw_data >>>>>> in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0010_CR1_GluC_Glc_4_rep2.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 9: 150624_0012_CR1_GluC_Xyl_0p4_rep3.pep.XMLWARNING: empty >>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0012_CR1_GluC_Xyl_0p4_rep3.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 10: 150624_0014_CR1_GluC_Xyl_4_rep3.pep.XMLWARNING: empty raw_data >>>>>> in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0014_CR1_GluC_Xyl_4_rep3.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 11: 150624_0015_CR1_GluC_Glc_0p4_rep3.pep.XMLWARNING: empty >>>>>> raw_data in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0015_CR1_GluC_Glc_0p4_rep3.mzXML >>>>>> in msms_run_summary tag ... >>>>>> file 12: 150624_0016_CR1_GluC_Glc_4_rep3.pep.XMLWARNING: empty raw_data >>>>>> in msms_run_summary tag ... trying mzML ... >>>>>> Failed to open input file >>>>>> 'c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzML'.WARNING: >>>>>> cannot open data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzML >>>>>> in msms_run_summary tag ...... trying .mzXML ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzXML >>>>>> in msms_run_summary tag ... >>>>>> SUCCESS: CORRECTED data file >>>>>> c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/150624_0016_CR1_GluC_Glc_4_rep3.mzXML >>>>>> in msms_run_summary tag ... >>>>>> processed altogether 186504 results >>>>>> INFO: Results written to file: >>>>>> C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml >>>>>> command completed in 86 sec >>>>>> >>>>>> running: "C:/TPP/bin/DatabaseParser >>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml"" >>>>>> command completed in 2 sec >>>>>> >>>>>> running: "C:/TPP/bin/RefreshParser >>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" >>>>>> "C:\Jesse\Ecoli.fasta"" >>>>>> - Searching the tree...opening "c:/Jesse/Ecoli.fasta" as >>>>>> "c:/Inetpub/wwwroot/ISB/data/2015/Kac_GluC/Ecoli.fasta" >>>>>> >>>>>> - Linking duplicate entries... - Printing results... >>>>>> >>>>>> - Building Commentz-Walter keyword tree...command completed in 22 sec >>>>>> >>>>>> running: "C:/TPP/bin/PeptideProphetParser >>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 >>>>>> CLEVEL=2.5 PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" >>>>>> using Accurate Mass Bins >>>>>> using PPM mass difference >>>>>> using pI >>>>>> Using Decoy Label "XXX_". >>>>>> Ignoring charge 1+ spectra. >>>>>> Not using ntt model >>>>>> Using non-parametric distributions >>>>>> (MS-GF+)WARNING: Support of MSGF+ may not be full. There exist known >>>>>> issues with the way MSGF+ encodes certain modifications in pep.xml that >>>>>> may not be correct. Also, high-scoring DECOY have been observed in MSGF+ >>>>>> analysis. The user is encouraged to be vigilant in comparing model >>>>>> estimated error-rates to the DECOY-estimated error-rates to make sure >>>>>> the two agree and set CLEVEL parameter accordingly: see >>>>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#What_is_CLEVEL_and_when_do_I_use_it.3F >>>>>> adding Accurate Mass mixture distr >>>>>> adding pI mixture distr >>>>>> init with MS-GF+ nonspecific >>>>>> >>>>>> command "C:/TPP/bin/PeptideProphetParser >>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 >>>>>> CLEVEL=2.5 PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" >>>>>> failed: Unknown error >>>>>> >>>>>> command "C:/TPP/bin/PeptideProphetParser >>>>>> "C:/tmp/a03524/2015/Kac_GluC/test.interact.pep.xml" MINPROB=0.05 >>>>>> CLEVEL=2.5 PPM PPM ACCMASS PI NONTT NONPARAM DECOY=XXX_ IGNORECHG=1" >>>>>> exited with non-zero exit code: 255 >>>>>> QUIT - the job is incomplete >>>>>> >>>>>> >>>>>> On Thursday, July 9, 2015 at 2:33:16 PM UTC-7, [email protected] >>>>>> wrote: >>>>>>> >>>>>>> Hi David, >>>>>>> >>>>>>> I can cope with the command line. Thanks for the info I never would >>>>>>> have worked that one out... >>>>>>> >>>>>>> Peter >>>>>>> >>>>>>> On Thursday, July 9, 2015 at 2:55:41 PM UTC+10, [email protected] >>>>>>> wrote: >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> >>>>>>>> I want to use the TPP to combine, Mascot, X!Tandem and MSGF+ >>>>>>>> searches (amongst other things). I'm having trouble getting around >>>>>>>> some of >>>>>>>> the basics. I have successfully used the TPP in the past to process >>>>>>>> samples, but only with Mascot data. >>>>>>>> >>>>>>>> Once I get my MSGF+ output files converted to pepXML I should be >>>>>>>> fine. I cannot work out how I get the MSGF+ files converted. The >>>>>>>> output >>>>>>>> generated by MSGF+ is an mzid file. I am also unclear as to where the >>>>>>>> database (with decoys) and mzXML files, used for searching, need to be >>>>>>>> located when generating this pepXML file. I have noticed error >>>>>>>> messages in >>>>>>>> the logs about accessing the database and mzXML file. I am generally >>>>>>>> using >>>>>>>> the Petunia interface as it's much nicer to work with multiple files. >>>>>>>> >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> >>>>>>>> Peter >>>>>>>> >>>>>>> -- >>>>>> 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] <javascript:>. >>>>>> To post to this group, send email to [email protected] >>>>>> <javascript:>. >>>>>> 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] <javascript:>. >>>>> To post to this group, send email to [email protected] >>>>> <javascript:>. >>>>> 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] <javascript:>. >>>> To post to this group, send email to [email protected] >>>> <javascript:>. >>>> 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] <javascript:>. >>> To post to this group, send email to [email protected] >>> <javascript:>. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >> >> -- >> Joe Slagel >> Institute for Systems Biology >> [email protected] <javascript:> >> >> -- >> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
