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
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