Hi Sarah, Try double-checking two things:
1. In the Filtering Options section, ensure that "Proteins" is selected where it says, "Please specify whether the restriction file listed in step 3 above contains Proteins or Peptides." 2. Make sure your protein restriction list contains only a single column of IPI identifiers, e.g.: IPI00315309 IPI00330840 IPI00119970 IPI00127042 IPI00136935 IPI00138967 IPI00131972 If neither of these steps do the trick, please post the entire thread of output (i.e. including the 102 lines that we skipped), so I can get a better idea of where the problem is occuring. Hope this helps! Carly Martin Group Institute for Systems Biology On Oct 7, 8:40 am, Sarah <[email protected]> wrote: > Hey all, > > I have to say I am not too tech-savvy but think I took the right steps > in trying to create a list of MRM transitions with the MaRiMba tool. > > I have installed TPP v4.1 MaRiMba rev1 (on a windows operating system) > and it does create me a MRM list when I feed in the spectral library > and database with the mix of 18 proteins that were included as files > within the software package. > It also gives out MRM transitions when I put in as spectral library > NIST_human_IT_v3.0_2009_02_04_7AA.splib and as database the human IPI > database (ipi.HUMAN.v3.64.fasta) without restricting to specific > proteins. > But then when I specify a protein restriction list, I always end up > with 0 transitions. I do use the same format as the input ipi and I > even copied the whole ipi file from the database into a text file > (.txt) to make sure I have the exact same format as the database. But > still 0 mrms... > > This is the output I got with the above input: > > run_marimba.pl -t10 -s3 -k -m300 -M1200 -R c:/Inetpub/wwwroot/ISB/data/ > complete.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 > ________________________________________ > Run MaRiMba started at: Wed Oct 7 09:31:42 2009 > ...Refreshing library against database > ...Filtering out non-proteotypic and unmapped peptides in a tryptic > context only > SpectraST started at Wed Oct 07 09:31:42 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... > 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...63500...64000...64500...65000...65500...66000...66500...67000...67500...68000...68500...69000...69500...70000...70500...71000...71500...72000...72500...73000...73500...74000...74500...75000...75500...76000...76500...77000...77500...78000...78500...79000...79500...80000...80500...81000...81500...82000...82500...83000...83500...84000...84500...85000...85500...86000...86500...87000...87500...88000...88500...89000...89500...90000...90500...91000...91500...92000...92500...93000...93500...94000...94500...95000...95500...96000...96500...97000...97500...98000...98500...99000...99500...100000...100500...101000...101500...102000...102500...103000...103500...104000...104500...105000...105500...106000...106500...107000...107500...108000...108500...109000...109500...110000...110500...111000...111500...112000...112500...113000...113500...114000...114500...115000...115500...116000...116500...117000...117500...118000...118500...119000...119500...120000...120500...121000...121500...122000...122500...123000...123500...124000...124500...125000...125500...126000...126500...127000...127500...128000...128500...129000...129500...130000...130500...131000...131500...132000...132500...133000...133500...134000...134500...135000...135500...136000...136500...137000...137500...138000...138500...139000...139500...140000...140500...141000...141500...142000...142500...143000...143500...144000...144500...145000...145500...146000...146500...147000...147500...148000...148500...149000...149500...150000...150500...151000...151500...152000...152500...153000...153500...154000...154500...155000...155500...156000...156500...157000...157500...158000...158500...159000...159500...160000...160500...161000...161500...162000...162500...163000...163500...164000...164500...165000...165500...166000...166500...167000...167500...168000...168500...169000...169500...170000...170500...171000...171500...172000...172500...173000...173500...174000...174500...175000...175500...176000...176500...177000...177500...178000...178500...179000...179500...180000...180500...181000...181500...182000...182500...183000...183500...184000...184500...185000...185500...186000...186500...187000...187500...188000...188500...189000...189500...190000...190500...191000...191500...192000...192500...193000...193500...194000...194500...195000...195500...196000...196500...197000...197500...198000...198500...199000...199500...200000...200500...201000...201500...202000...202500...203000...203500...204000...204500...205000...205500...206000...206500...207000...207500...208000...208500...209000...209500...210000...210500...211000...211500...212000...212500...213000...213500...214000...214500...215000...215500...216000...216500...217000...217500...218000...218500...219000...219500...220000...220500...221000...221500...222000...222500...223000...223500...224000...224500...225000...225500...226000...226500...227000...227500...228000...228500...229000...229500...230000...230500...231000...231500...232000...232500...233000...233500...234000...234500...235000...235500...236000...236500...237000...237500...238000...238500...239000...239500...240000...240500...241000...241500...242000...242500...243000...243500...244000...244500...245000...245500...246000...246500...247000...247500...248000...248500...249000...249500...250000...250500...251000...251500...252000...252500...253000...253500...254000...254500...255000...255500...256000...256500...257000...257500...258000...258500...259000...259500...260000...260500...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: 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 > > ________________________________________ > ...skipping 102 lines of output... > ________________________________________ > MRM Table file "tmp_MRM.mrm" 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 = 0 seconds. > SpectraST finished at Wed Oct 07 09:48:09 2009 without error. > ...Applying user-defined fiters > ...Sorting results > ...Restricting to minimum number of transitions per peptide > ...Deleting temporary files > Job finished at: Wed Oct 7 09:48:12 2009 > > Command Successful > > I don't know if that helps.. > > I would really appreciate any ideas!! > > Thanks, Sarah --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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