Carly, thanks again for your help, MaRiMba is running with the "adjusted" IPI human fasta file library!
Brendan, thanks for the advice, I just looked at the tutorials and will for sure try it out. I will let you know how things go. sarah > Date: Thu, 8 Oct 2009 07:30:21 -0700 > Subject: [spctools-discuss] Re: MaRiMba does not give out MRM transitions > From: [email protected] > To: [email protected] > > > Hi Sarah and Carly, > I have been a development contributor to the TPP, X! Tandem, CPAS and > ProteoWizard open source proteomics software projects. > > As a member of the MacCoss Lab at the University of Washington for the > past year, I have been working on software for MRM method building and > data analysis called Skyline which is freely available at: > > http://proteome.gs.washington.edu/software/skyline > > And under open source development as part of the ProteoWizard project: > > http://proteowizard.sourceforge.net/ > > Carly, if you would like to post a similar announcement of the > availability of MaRiMba to the Skyline support board, please feel > free. I know we are both trying to provide the best possible software > to advance the study of proteomics, and I hope we can benefit from > each other's insights as we work in the forum of open source academic > software. > > Sarah, I'd be interested to hear your impressions, if you are willing > to try both. > > --Brendan > > On Oct 7, 5:18 pm, Carly <[email protected]> wrote: > > Hi Sarah, > > > > Can you send me your protein list and an excerpt from your protein > > database? I still suspect it's some sort of identifier mismatch issue, > > especially given that your peptides/transitions are lost at the step > > of creating the protein-restricted library. > > > > Thanks! > > > > Carly > > > > On Oct 7, 2:09 pm, Sarah <[email protected]> wrote: > > > > > Hi Carly, > > > > > thanks for your ideas. Unfortunately, still no transitions on my > > > list....I did make sure the "protein" box was checked and also created > > > a new list with IPI identifiers (the IPI identifier in the format > > > IPI00123456 is sufficient, right?) to double check the format. This is > > > the log for this search: > > > > > # Commands for session MV240KSZQ on Wed Oct 7 16:44:07 2009 > > > # BEGIN COMMAND BLOCK > > > ###### BEGIN Command Execution ###### > > > [Wed Oct 7 16:44:08 2009] EXECUTING: run_marimba.pl -t10 -s3 -k -m300 > > > -M1200 -R c:/Inetpub/wwwroot/ISB/data/IPIwhole.txt -X C,M -T Q -i y -z > > > 2,3 -Z 1,2 c:/Inetpub/wwwroot/ISB/data/MaRiMba/ > > > NIST_human_IT_v3.0_2009_02_04_7AA.splib c:/Inetpub/wwwroot/ISB/data/ > > > ipi.HUMAN.v3.64.fasta c:/Inetpub/wwwroot/ISB/data/MRMlist.txt > > > OUTPUT: > > > Run MaRiMba started at: Wed Oct 7 16:44:08 2009 > > > ...Refreshing library against database > > > ...Filtering out non-proteotypic and unmapped peptides in a tryptic > > > context only > > > SpectraST started at Wed Oct 07 16:44:08 2009. > > > Creating library from "c:/Inetpub/wwwroot/ISB/data/MaRiMba/ > > > NIST_human_IT_v3.0_2009_02_04_7AA.splib" > > > REFRESHING protein mappings...DONE! > > > Importing peptide ions... > > > 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> > > > > 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: 63094 > > > Total number of distinct peptide ions in library: 63094 > > > Total number of distinct stripped peptides in library: 37177 > > > CHARGE +1: 4595 ; +2: 34631 ; +3: 20407 > > > TERMINI Tryptic: 63094 ; Semi-tryptic: 0 ; Non-tryptic: 0 > > > METHIONINE MOD Oxidized: 8160 > > > CYSTEINE MOD CAM: 9231 ; Cleavable-ICAT: 1181 ; Uncleavable-ICAT: > > > 1453 > > > PROBABILITY >0.9999: 47423 ; 0.999-0.9999: 9010 ; 0.99-0.999: > > > 4724 ; 0.9-0.99: 1937 <0.9: 0 > > > NREPS 20+: 11473 ; 10-19: 8857 ; 4-9: 18596 ; 2-3: 24168 ; > > > 1: 0 > > > > > Total Run Time = 938 seconds. > > > SpectraST finished at Wed Oct 07 16:59:46 2009 without error. > > > ...Restricting input library to proteins on list > > > SpectraST started at Wed Oct 07 16:59:46 2009. > > > Creating library from "c://tmp_refreshed.splib" > > > Importing peptide ions... > > > 500...1000...1500...2000...2500...3000...3500...4000...4500...5000...5500...6000...6500...7000...7500...8000...8500...9000...9500...10000...10500...11000...11500...12000...12500...13000...13500...14000...14500...15000...15500...16000...16500...17000...17500...18000...18500...19000...19500...20000...20500...21000...21500...22000...22500...23000...23500...24000...24500...25000...25500...26000...26500...27000...27500...28000...28500...29000...29500...30000...30500...31000...31500...32000...32500...33000...33500...34000...34500...35000...35500...36000...36500...37000...37500...38000...38500...39000...39500...40000...40500...41000...41500...42000...42500...43000...43500...44000...44500...45000...45500...46000...46500...47000...47500...48000...48500...49000...49500...50000...50500...51000...51500...52000...52500...53000...53500...54000...54500...55000...55500...56000...56500...57000...57500...58000...58500...59000...59500...60000...60500...61000...61500...62000...62500...63000...DONE! > > > > > Library file (BINARY) "tmp_restricted.splib" created. > > > Library file (TEXT) "tmp_restricted.sptxt" created. > > > M/Z Index file "tmp_restricted.spidx" created. > > > Peptide Index file "tmp_restricted.pepidx" created. > > > > > Total number of spectra in library: 0 > > > Total number of distinct peptide ions in library: 0 > > > Total number of distinct stripped peptides in library: 0 > > > CHARGE +1: 0 ; +2: 0 ; +3: 0 > > > TERMINI Tryptic: 0 ; Semi-tryptic: 0 ; Non-tryptic: 0 > > > METHIONINE MOD Oxidized: 0 > > > CYSTEINE MOD CAM: 0 ; Cleavable-ICAT: 0 ; Uncleavable-ICAT: 0 > > > PROBABILITY >0.9999: 0 ; 0.999-0.9999: 0 ; 0.99-0.999: 0 ; > > > 0.9-0.99: 0 <0.9: 0 > > > NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 0 > > > > > Total Run Time = 110 seconds. > > > SpectraST finished at Wed Oct 07 17:01:36 2009 without error. > > > ...Creating consensus library > > > SpectraST started at Wed Oct 07 17:01:36 2009. > > > Creating CONSENSUS library from "c://tmp_restricted.splib" > > > Importing peptide ions...DONE! > > > > > Library file (BINARY) "tmp_consensus.splib" created. > > > Library file (TEXT) "tmp_consensus.sptxt" created. > > > M/Z Index file "tmp_consensus.spidx" created. > > > Peptide Index file "tmp_consensus.pepidx" created. > > > > > Total number of spectra in library: 0 > > > Total number of distinct peptide ions in library: 0 > > > Total number of distinct stripped peptides in library: 0 > > > CHARGE +1: 0 ; +2: 0 ; +3: 0 > > > TERMINI Tryptic: 0 ; Semi-tryptic: 0 ; Non-tryptic: 0 > > > METHIONINE MOD Oxidized: 0 > > > CYSTEINE MOD CAM: 0 ; Cleavable-ICAT: 0 ; Uncleavable-ICAT: 0 > > > PROBABILITY >0.9999: 0 ; 0.999-0.9999: 0 ; 0.99-0.999: 0 ; > > > 0.9-0.99: 0 <0.9: 0 > > > NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 0 > > > > > Total Run > > > > ... > > > > read more » > > _________________________________________________________________ http://redirect.gimas.net/?n=M0910xHerbstmode2 So gehst du mir nicht vor die Tür! 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