Hi Everyone, I am using SpectraST (version 5.0, TPP v5.1.0 Syzygy, Build 201806211802-exported (Linux-x86_64)) on Lumos DDA data. I have searched for Acetyl(K) and Trimethyl(K) using Comet and i have my interprophet file which I am running through Spectrast.
My mods are defined below: variable_mod04 = 42.046950 K 0 3 -1 0 variable_mod05 = 42.010565 K 0 3 -1 0 This is how my spectrast.usermods looks: R|+14.0157| R|+28.0313| K|+14.0157| K|+28.0313| K|+42.046950| K|+42.010565| This is my spectrast command line: START: (Thu Jul 12 11:41:37 2018) spectrast -c_BIN! -cfProtein!~DECOY_ -cP0.994759 -M/common/venkatramanv/Data/Params/SpectrastParams/spectrast.usermods -cN/common/robinsonax/Data/18_7_LUMOS_Methyl_Combined/spectrast/18_7_Lumos_Methyl_Combined_SpecLib /common/robinsonax/Data/18_7_LUMOS_Methyl_Combined/msconvert/18_7_Lumos_Methyl_Combined.iprophet.pep.xml GENERAL: File offset size is 8 bytes. Big library supported. GENERAL: Pointer size is 8 bytes. GENERAL: Loading user-defined modifications from "/common/venkatramanv/Data/Params/SpectrastParams/spectrast.usermods" . GENERAL: Modification R|+14.0157| successfully added as R[170]|14.0157|Methyl . GENERAL: Modification R|+28.0313| successfully added as R[184]|28.0313|Dimethyl . GENERAL: Modification K|+14.0157| successfully added as K[142]|14.0157|Methyl . GENERAL: Modification K|+28.0313| successfully added as K[156]|28.0313|Dimethyl . GENERAL: Modification K|+42.046950| successfully added as K[170]|42.0106|Acetyl . GENERAL: Modification K|+42.010565| successfully added as K[170]|42.0106|Acetyl . Even though i have explicitly specified +42.046950 and +42.010565, it adds both as Acetyl and only detects Acetyl. It is unable to separate Acetyl and Trimethyl even though unimod.xml has the mass specified as the ones I am using. SpectraST started at Thu Jul 12 12:14:26 2018. Processing "/common/robinsonax/Data/18_7_LUMOS_Methyl_Combined/msconvert/18_7_Lumos_Methyl_Combined.iprophet.pep.xml" Importing all spectra with P>=0.994759 ...10%...20%...30%...40%...50%...60%...70%...80%...90%...DONE! Library file "/common/robinsonax/Data/18_7_LUMOS_Methyl_Combined/spectrast/18_7_Lumos_Methyl_Combined_SpecLib.splib" created. M/Z Index file "/common/robinsonax/Data/18_7_LUMOS_Methyl_Combined/spectrast/18_7_Lumos_Methyl_Combined_SpecLib.spidx" created. Peptide Index file "/common/robinsonax/Data/18_7_LUMOS_Methyl_Combined/spectrast/18_7_Lumos_Methyl_Combined_SpecLib.pepidx" created. Total number of spectra in library: 285413 Total number of distinct peptide ions in library: 35663 Total number of distinct stripped peptides in library: 27326 CHARGE +1: 0 ; +2: 186099 ; +3: 87012 ; +4: 11022 ; +5: 1149 ; >+5: 131 ; Unk: 0 TERMINI Tryptic: 284075 ; Semi-tryptic: 1338 ; Non-tryptic: 0 PROBABILITY >0.9999: 210762 ; 0.999-0.9999: 48465 ; 0.99-0.999: 26186 ; 0.9-0.99: 0 ; <0.9: 0 NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 285413 MODIFICATIONS C,Carbamidomethyl: 60438 K,Acetyl: 354 ; K,Dimethyl: 234 ; K,Methyl: 177 M,Oxidation: 6775 R,Dimethyl: 156 ; R,Methyl: 122 n,Acetyl: 1 Total Run Time = 2996 seconds. SpectraST finished at Thu Jul 12 13:04:22 2018 without error. Has anyone faced this issue with spectrast? Can i get any pointers on how i can make spectrast differentiate the two? Regards Vidya -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.