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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