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.
