Dear Friends,
I have mass-spec data for a 13C isotope for a compound:
**note compound compoundId formula expectedRtDiff ppmDiff parent 091215_0i**
C12 PARENT Acetyl CoA HMDB01206 C23H38N7O17P3S 0.004406929 0.7552748 808.1191 5367.899
C13-label-1 Acetyl CoA HMDB01206 C23H38N7O17P3S 0.01298141 1.206941 808.1191 1003.555
C13-label-2 Acetyl CoA HMDB01206 C23H38N7O17P3S 0.006209373 0.0753404 808.1191 131.6266
C13-label-3 Acetyl CoA HMDB01206 C23H38N7O17P3S 0.001900673 1.35445 808.1191 0
C13-label-6 Acetyl CoA HMDB01206 C23H38N7O17P3S 0.09920025 6.447333 808.1191 0
C13-label-7 Acetyl CoA HMDB01206 C23H38N7O17P3S 9.918213E-05 7.412795 808.1191 0
C13-label-15 Acetyl CoA HMDB01206 C23H38N7O17P3S 0.05370045 6.895632 808.1191 0
C13-label-18 Acetyl CoA HMDB01206 C23H38N7O17P3S 0.07200146 0.07387644 808.1191 0
C13-label-19 Acetyl CoA HMDB01206 C23H38N7O17P3S 0.06890011 3.24662 808.1191 0
C13-label-20 Acetyl CoA HMDB01206 C23H38N7O17P3S 0.0965004 5.011425 808.1191 0
In the above file "C13-label-1" means 1 occurrence of C13 isotope for the respective compound, likewise other C13 notations - C13-label-2, etc. I prepared the files for ICT (https://github.com/jungreuc/isotope_correction_toolbox) correction run, for all C13 isotopes.
The "chemical-data" file:
AcetylCoA:Precursor:13C1,H38,N7,O17,P3,S1,C22
AcetylCoA:Product Ion:13C1,H38,N7,O17,P3,S1,C22
AcetylCoA:Precursor:13C2,H38,N7,O17,P3,S1,C21
AcetylCoA:Product Ion:13C2,H38,N7,O17,P3,S1,C21
AcetylCoA:Precursor:13C3,H38,N7,O17,P3,S1,C20
AcetylCoA:Product Ion:13C3,H38,N7,O17,P3,S1,C20
AcetylCoA:Precursor:13C6,H38,N7,O17,P3,S1,C17
AcetylCoA:Product Ion:13C6,H38,N7,O17,P3,S1,C17
AcetylCoA:Precursor:13C7,H38,N7,O17,P3,S1,C16
AcetylCoA:Product Ion:13C7,H38,N7,O17,P3,S1,C16
AcetylCoA:Precursor:13C15,H38,N7,O17,P3,S1,C8
AcetylCoA:Product Ion:13C15,H38,N7,O17,P3,S1,C8
AcetylCoA:Precursor:13C18,H38,N7,O17,P3,S1,C5
AcetylCoA:Product Ion:13C18,H38,N7,O17,P3,S1,C5
AcetylCoA:Precursor:13C19,H38,N7,O17,P3,S1,C4
AcetylCoA:Product Ion:13C19,H38,N7,O17,P3,S1,C4
AcetylCoA:Precursor:13C20,H38,N7,O17,P3,S1,C3
AcetylCoA:Product Ion:13C20,H38,N7,O17,P3,S1,C3
And the "mass-spec" data file:
AcetylCoA_M0 1003.555
AcetylCoA_M1 131.6266
AcetylCoA_M2 0
AcetylCoA_M3 0
AcetylCoA_M4 0
AcetylCoA_M5 0
AcetylCoA_M6 0
AcetylCoA_M7 0
AcetylCoA_M8 0
When running ICT:
ict.pl -c chemical-data.txt -m mass-spec.txt -o correct.data
it gives error:
INFO: Bio::IsotopeCorrection::NaturalIsotopes::new: Found 7 internal isotope data sets at isotope_correction_toolbox-master/Bio/IsotopeCorrection/NaturalIsotopes.pm line 57, <DATA> line 7.
Do correction for compound 0 'AcetylCoA'. Number of tof experiments found: 1.
INFO: Bio::IsotopeCorrection::Chemicals::new: going to open file 'tmp_chem_AcetylCoA_0.txt' for reading ... at isotope_correction_toolbox-master/Bio/IsotopeCorrection/Chemicals.pm line 62.
INFO: Bio::IsotopeCorrection::Chemicals::_process_data_sets: rel_mass_tracer_isotope=1
INFO: Bio::IsotopeCorrection::Chemicals::_process_data_sets: rel_mass_tracer_isotope=1
INFO: Bio::IsotopeCorrection::Chemicals::_process_data_sets: is_isotopologue: 1
DEBUG: Bio::IsotopeCorrection::Chemicals::_process_data_sets: exluding element: O
DEBUG: Bio::IsotopeCorrection::Chemicals::_process_data_sets: exluding element: S
DEBUG: Bio::IsotopeCorrection::Chemicals::_process_data_sets: exluding element: H
DEBUG: Bio::IsotopeCorrection::Chemicals::_process_data_sets: exluding element: N
DEBUG: Bio::IsotopeCorrection::Chemicals::_process_data_sets: exluding element: P
DEBUG: Bio::IsotopeCorrection::Chemicals::_process_data_sets: exluding element: C
INFO: Bio::IsotopeCorrection::Chemicals::new: going to open file 'tmp_tof_AcetylCoA_0.txt' for reading ... at isotope_correction_toolbox-master/Bio/IsotopeCorrection/Chemicals.pm line 81.
INFO: Bio::IsotopeCorrection::Chemicals::_compute_tracer_iso_matrix: entered
INFO: Bio::IsotopeCorrection::Chemicals::_compute_tracer_iso_matrix: tracer element 'C'
INFO: Bio::IsotopeCorrection::Chemicals::_compute_tracer_iso_matrix: tracer element 'C13'
ERROR: number of measured TOF values (9) is not equal to number of non-zero elements in isotope matrix (21) at isotope_correction_toolbox-master/ict.pl line 80.
INFO: Bio::IsotopeCorrection::Chemicals::_compute_tracer_iso_matrix: leaving
ERROR: Bio::IsotopeCorrection::Chemicals::_check_tof_values: didn't find measured value for M=9 and m=9, check your input file at isotope_correction_toolbox-master/Bio/IsotopeCorrection/Chemicals.pm line 2181.
I am trying to find what am I doing wrong? I would really appreciate your suggestions and comments to solve this issue. If something is not clear please let me know.
Thanks, DK