Question: Corrections of the peak areas of C13 isotopes of mass-spectrometry data using ICT package
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gravatar for DanielC
8 months ago by
DanielC90
Canada
DanielC90 wrote:

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

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