Hi Jum It's probably a too late reply for you, but may be helpful for others.
The problem could be that you don't have the SSRCalc3.par file. If you do though, then the perl program SSRCalc3.pl is not looking for it properly. This last option must be the most probable since all downloads of TPP contain the parameter file. To solve the problem you have to change a line in the source code of SSRCalc3.pl, which in Windows is under "C:\Inetpub\tpp-bin\SSRCalc3.pl". Open it in an editior go to line 527 (or around) where says *my $infile = "SSRCalc3.par";* and change for *my $infile = "C:/Inetpub/tpp-bin/SSRCalc3.par";*. Save the changes and run Marimba again. Best, Victor. On Friday, April 29, 2011 3:31:33 PM UTC+2, jun wrote: > > Hi everyone, I am just a beginner in MRM and my first step end up in > mud. > > I am using TPP ver4.4.1 vuvuzela and downloaded the 18 protein MaRiMba > tutorial files. I followed the instructions in the pdf files attached > with the tutorial files, then I saw the red "FAILED". According to the > log message, there is an error 9 with filterMRM. I did monor change to > the criteria used for filter and still could not get my first MRM > list. > > I attach the log message here and hope for your advices. > > Thank you all! > > > Run MaRiMba started at: Fri Apr 29 21:09:22 2011 > ...Refreshing library against database > ...Filtering out non-proteotypic and unmapped peptides > SpectraST started at Fri Apr 29 21:09:23 2011. > Creating library from "c:/Inetpub/wwwroot/ISB/data/MaRiMba/ > 18mix_Mix7_Raw.splib" > REFRESHING protein mappings...DONE! > Importing peptide ions...500...1000...DONE! > > Library file (BINARY) "tmp_refreshed.splib" created. > Library file (TEXT) "tmp_refreshed.sptxt" created. > M/Z Index file "tmp_refreshed.spidx" created. > Peptide Index file "tmp_refreshed.pepidx" created. > > Total number of spectra in library: 11679 > Total number of distinct peptide ions in library: 1107 > Total number of distinct stripped peptides in library: 811 > > CHARGE +1: 0 ; +2: 3742 ; +3: 4512 ; +4: 2591 ; +5: 834 ; > > +5: 0 > TERMINI Tryptic: 10334 ; Semi-tryptic: 1333 ; Non-tryptic: > 12 > PROBABILITY >0.9999: 5618 ; 0.999-0.9999: 2753 ; 0.99-0.999: > 1875 ; 0.9-0.99: 1432 <0.9: 1 > > > ...skipping 76 lines of output... > > Library file (BINARY) "tmp_MRM.splib" created. > Library file (TEXT) "tmp_MRM.sptxt" created. > M/Z Index file "tmp_MRM.spidx" created. > Peptide Index file "tmp_MRM.pepidx" created. > MRM Table file "tmp_MRM.mrm" created. > > Total number of spectra in library: 118 > Total number of distinct peptide ions in library: 118 > Total number of distinct stripped peptides in library: 88 > > CHARGE +1: 0 ; +2: 75 ; +3: 34 ; +4: 8 ; +5: 1 ; >+5: 0 > TERMINI Tryptic: 118 ; Semi-tryptic: 0 ; Non-tryptic: 0 > PROBABILITY >0.9999: 87 ; 0.999-0.9999: 15 ; 0.99-0.999: 11 ; > 0.9-0.99: 5 <0.9: 0 > NREPS 20+: 28 ; 10-19: 26 ; 4-9: 44 ; 2-3: 11 ; 1: 9 > MODIFICATIONS C,Carbamidomethyl: 36 > > Total Run Time = 0 seconds. > SpectraST finished at Fri Apr 29 21:12:16 2011 without error. > ...Applying user-defined fiters > ERROR: there was a problem with filterMRM: 9 > > Command FAILED -- 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.
