Rachel, I was able to run a Comet search through creating a SpectraST library so I took a look at your posted comet.iprohpet.pep.xml file and the problem is that, for some reason, your spectrum names are off. They look like
<spectrum_query spectrum=.07651.07651.2" whereas they should be something like <spectrum_query spectrum=QGP_QE_150226_03_IS207_DENV_HPep_iRT_PRM1.07651.07651.2" It's the missing base name that is causing SpectraST to try and read the spectra from ".mzXML" instead of "QGP_QE_150226_03_IS207_DENV_HPep_iRT_PRM1.mzXML". Can you look at your base Comet search output, e.g. the file QGP_QE_150226_03_IS207_DENV_HPep_iRT_PRM1.pep.xml, and report back what the "spectrum=" attribute value is? If it has the full expected string including the "QGP_QE...." base name, look at the PeptideProphet processed file and see if it has changed in there. - Jimmy On Tue, Mar 10, 2015 at 12:07 AM, Rachel <[email protected]> wrote: > Hi Jimmy, > > I just run spectrast in C:\inetpub\wwwroot\ISB\data\Dengue_comet\, still > can not. > > By the way, I always copy mzXML files in the folder to run spectrast. > > I attached the error and comet iprophet again. > > Please help. > > Thanks > Rachel > > On Thursday, March 5, 2015 at 3:26:21 PM UTC+8, Rachel wrote: > >> Dear Eric, >> I have run spectrast successfully on tandem iprophet output, but not on >> comet output. (using following command) >> what can be the reason? >> spectrast -cNSpectralib -cP0.0001 -cODengue_id.txt -cIHCD -cf "Protein! ~ >> DECOY" -c_IRTiRTdefinition.txt -c_IRR comet.iprophet.pep.xml >> >> Below is the log file... I am sure I have put all mzXML files in the same >> folder. >> ========== >> START: (Thu Mar 05 14:49:48 2015) spectrast -cNSpectralib -cP0.0001 >> -cODengue_id.txt -cIHCD -cf Protein! ~ DECOY -c_IRTiRTdefinition.txt -c_IRR >> comet.iprophet.pep.xml >> GENERAL: File offset size is 8 bytes. Big library supported. >> GENERAL: Pointer size is 8 bytes. >> CREATE: Apply FILTER for Protein! ~ DECOY >> CREATE: Apply FILTER for entries in protein list "c:/Users/Administrator/ >> Dengue/Dengue_id.txt" >> CREATE: IMPORT FROM PepXML "c:/Users/Administrator/ >> Dengue/comet.iprophet.pep.xml", (Comet against >> "Human_reviewed_CON_Selected_Denguevirus_iRT_DECOY.fasta" (AA); ) >> [P=0.0001;q=9999;n=;g=FALSE;o=FALSE;I=HCD;_RNT=0;_RDR= >> 100000;_DCN=0;_NAA=6;_NPK=10;_MDF=9999;_CEN=FALSE;_XAN= >> FALSE;_BRK=FALSE;_BRM=FALSE;_IRT=c:/Users/Administrator/ >> Dengue/iRTdefinition.txt;_IRR=TRUE]; FILTER for Protein! ~ DECOY; FILTER >> for entries in protein list "c:/Users/Administrator/Dengue/Dengue_id.txt" >> PEPXML IMPORT: Total of 46372 read (46011 with PeptideProphet >> probability; 46011 with iProphet probability). >> PEPXML IMPORT: Total of 22230 spectra (46011 queries) have probability >= >> 0.0001. >> PEPXML IMPORT: Read RT landmarks from file >> "c:/Users/Administrator/Dengue/iRTdefinition.txt" >> : LGGNEQVTR (29.3) | GAGSSEPVTGLDAK (42.4) | VEATFGVDESNAK (52.7) | >> YILAGVENSK (50.6) | TPVISGGPYEYR (54.7) | TPVITGAPYEYR (58.1) | >> DGLDAASYYAPVR (68.9) | ADVTPADFSEWSK (69.1) | GTFIIDPGGVIR (77.9) | >> GTFIIDPAAVIR (86.1) | LFLQFGAQGSPFLK (87.8) | . >> PEPXML IMPORT: RT normalization by linear regression. Found 10 landmarks >> in MS run "". >> PEPXML_IMPORT: Final fitted equation: iRT = (rRT + 38.32) / (61.4); R^2 = >> 0.9956; 0 outliers removed. >> ERROR PEPXML IMPORT: Cannot open file ".mzXML|.mzML|.mzXML.gz|.mzML.gz|.mz5 >> in c:/Users/Administrator/Dengue/". No scan from this file will be >> imported. >> ========== >> Thank you! >> Rachel >> > -- > 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.
