Hello Rachel, It seems that the iProphet file does not contain a named "MS run" (i.e. the base name of the originating data file), and so it fails to find the corresponding mzXML files. A couple of questions: what version of Comet are you using? (you can find out by typing 'comet -v' on the command-line. Are you able to share your comet.pep.xml files so we can see where the error may have happened? Cheers, --Luis
On Wed, Mar 4, 2015 at 11:26 PM, Rachel <[email protected]> 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.
