Thanks a lot, Brendan!! I'll start with SkyLine.
On 5月26日, 上午12时27分, Brendan MacLean <[email protected]> wrote: > 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- 隐藏被引用文字 - > > - 显示引用的文字 - -- 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.
