Hi Jun, Unfortunately, there is no longer any active development being applied to MaRiMba. Its creator, Carly Holstein (Sherwood), has returned to graduate school in another discipline. Even she was using the open source software I have been working on for the past 3 years, called Skyline, for working with MRM methods and data analysis:
http://proteome.gs.washington.edu/software/skyline I think it is clear she had a positive experience with Skyline from her final proteomics publication: http://www.ncbi.nlm.nih.gov/pubmed/20968307 If you prefer to stick with ISB software, or really want to work with a web server and browser-based user interface, the ISB tool under active development for targeted proteomics is called ATAQS: http://tools.proteomecenter.org/ATAQS/ATAQS.html Good luck with your investigations. I hope one of these tools will be of use to you. --Brendan On May 25, 12:42 am, jun <[email protected]> wrote: > almost a month has pased since I posted this, maybe it has been > discussed before. > can somebody light me up with the link to the previous post? > or > just tell me how to eliminate the "ERROR: there was a problem with > filterMRM: 9 "? > > Thank you for all your time and attention! > > On 4月29日, 下午9时31分, jun <[email protected]> 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 post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
