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 » --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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