Mercurial > repos > gmat > isocor
changeset 1:fa183805db31 draft default tip
"planemo upload"
| author | gmat |
|---|---|
| date | Mon, 04 May 2020 11:38:09 -0400 |
| parents | 96f7617b4848 |
| children | |
| files | isocor.xml test-data/Metabolites.dat test-data/results.log test-data/results.tsv |
| diffstat | 4 files changed, 249 insertions(+), 212 deletions(-) [+] |
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--- a/isocor.xml Mon May 27 03:33:36 2019 -0400 +++ b/isocor.xml Mon May 04 11:38:09 2020 -0400 @@ -1,22 +1,22 @@ -<tool id="isocor" name="Isotope Correction for mass spectrometry labeling experiments" version="0.1.2"> +<tool id="isocor" name="Isotope Correction for mass spectrometry labeling experiments" version="0.1.3"> <requirements> - <requirement type="package" version="2.1.3">isocor</requirement> + <requirement type="package" version="2.2.0">isocor</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - isocorcli -t "$tracer" -M "$input1" -D "$input2" -I "$input3" -#if $tracer_purity: - -p $tracer_purity + isocorcli -t "$tracer" -M "$db.input1" -D "$db.input2" -I "$db.input3" +#if $tcorrection.tracer_purity: + -p $tcorrection.tracer_purity #end if -#if $resolution: - -r $resolution +#if $HR.resolution: + -r $HR.resolution #end if -#if $mz: - -m $mz +#if $HR.mz: + -m $HR.mz #end if -#if $resolution_formula_code: - -f $resolution_formula_code +#if $HR.resolution_formula_code: + -f $HR.resolution_formula_code #end if -#if $correct_na_tracer: +#if $tcorrection.correct_na_tracer: -n #end if #if $verbose_log: @@ -26,45 +26,81 @@ ]]></command> <inputs> <param type="text" name="tracer" argument="-t" label="the isotopic tracer (e.g. '13C')" /> - <param type="data" name="input1" argument="-M" label="metabolites db" format="tabular" /> - <param type="data" name="input2" argument="-D" label="derivatives db" format="tabular" /> - <param type="data" name="input3" argument="-I" label="isotopes db" format="csv" /> - <param type="integer" optional="true" argument="-r" name="resolution" label="HR only: resolution of the mass spectrometer (e.g. 1e4)" /> - <param type="integer" optional="true" argument="-m" name="mz" label="HR only: mz at which resolution is given (e.g. '400')" /> - <param type="boolean" optional="true" argument="-n" name="correct_na_tracer" label="flag to correct tracer natural abundance" /> - <param type="boolean" optional="true" argument="-v" name="verbose_log" label="flag to enable verbose logs" /> - <param type="text" optional="true" argument="-p" name="tracer_purity" label="purity vector of the tracer" /> + <param type="data" name="input4" label="measurements Data file" format="tabular" help="This file contains the raw MS data for each metabolite of each sample." /> + <section name="db" title="Database Files" expanded="true" help="The exact mass and natural abundance of each isotope and the elemental formulas used for correction have to be defined carefully, otherwise the correction will be wrong. IsoCor rely on several flat-files to store this information. Pre-configured files are shipped with IsoCor. For a good start download them on github"> + <param type="data" name="input1" argument="-M" label="metabolites db" format="tabular" /> + <param type="data" name="input2" argument="-D" label="derivatives db" format="tabular" /> + <param type="data" name="input3" argument="-I" label="isotopes db" format="csv" /> + </section> + <section name="HR" title="High Resolution Parameters" expanded="true" help="For measurements collected at high or ultrahigh resolution (e.g. on Orbitrap or FT-ICR instruments). Measurements collected at unitary resolution (e.g. on quadrupole instruments) are Low Resolution, don't fill this section."> + <param name="resolution_formula_code" optional="true" argument="-f" type="select" label="HR only: spectrometer formula code"> + <option value="orbitrap">Orbitrap</option> + <option value="ft-icr">ft-icr</option> + <option value="constant">Constant</option> + <option value="datafile">Datafile</option> + </param> + <param type="integer" optional="true" argument="-r" name="resolution" label="HR only: resolution of the mass spectrometer (e.g. '60000' or '1e4')" /> + <param type="integer" optional="true" argument="-m" name="mz" label="HR only: mz at which resolution is given (e.g. '400')" /> + </section> + <section name="tcorrection" title="Tracer Correction Options" expanded="true"> + <param type="boolean" optional="true" argument="-n" name="correct_na_tracer" label="flag to correct tracer natural abundance" help="Correct for the contribution of naturally occurring isotopes of the tracer element at unlabeled positions. This only concerns the tracer element: natural abundance of other elements is always corrected." /> + <param type="text" optional="true" argument="-p" name="tracer_purity" label="purity vector of the tracer (e.g. '0,0,0.99,0.01')" help="Correct for the contribution of isotopic impurities of the tracer at labeled positions. The isotopic purity is typically obtained from the manufacturer. e.g. ¹³C-substates with purity of 99%, use 0.01 for ¹²C and 0.99 for ¹³C." /> + </section> + <param type="boolean" optional="true" argument="-v" name="verbose_log" label="flag to enable verbose logs" help="Useful in case of trouble. Join it to the issue on github." /> - <param name="resolution_formula_code" optional="true" argument="-f" type="select" label="HR only: spectrometer formula code"> - <option value="orbitrap">Orbitrap</option> - <option value="ft-icr">ft-icr</option> - <option value="constant">Constant</option> - <option value="datafile">Datafile</option> - </param> - <param type="data" name="input4" label="measurements Data file" format="tabular" /> </inputs> <outputs> - <data name="output1" label="corrected measurements data file" format="csv" /> + <data name="output1" label="corrected measurements data file" format="tabular" /> <data name="output2" label="processing log file" format="txt" /> </outputs> <tests> <test> <param name="tracer" value="13C"/> - <param name="input1" value="Metabolites.dat"/> - <param name="input2" value="Derivatives.dat"/> - <param name="input3" value="Isotopes.dat"/> + <section name="db"> + <param name="input1" value="Metabolites.dat"/> + <param name="input2" value="Derivatives.dat"/> + <param name="input3" value="Isotopes.dat"/> + </section> <param name="input4" value="Data_example.tsv"/> <output name="output1"> - <assert_contents> - <has_n_columns n="9" /> - </assert_contents> - </output> + <assert_contents> + <has_n_columns n="10" /> + </assert_contents> + </output> <output name="output2"> - <assert_contents> - <has_text text="- root - INFO - errors: 0" /> - </assert_contents> - </output> + <assert_contents> + <has_text text="- root - INFO - errors: 0" /> + </assert_contents> + </output> + </test> + <test> + <param name="tracer" value="13C"/> + <section name="db"> + <param name="input1" value="Metabolites.dat"/> + <param name="input2" value="Derivatives.dat"/> + <param name="input3" value="Isotopes.dat"/> + </section> + <section name="HR"> + <param name="mz" value="400"/> + <param name="resolution" value="60000"/> + <param name="resolution_formula_code" value="orbitrap"/> + </section> + <section name="tcorrection"> + <param name="correct_na_tracer" value="-n"/> + <param name="tracer_purity" value="0.01,0.99"/> + </section> + <param name="input4" value="Data_example.tsv"/> + <output name="output1"> + <assert_contents> + <has_n_columns n="10" /> + </assert_contents> + </output> + <output name="output2"> + <assert_contents> + <has_text text="- root - INFO - errors: 0" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[
--- a/test-data/Metabolites.dat Mon May 27 03:33:36 2019 -0400 +++ b/test-data/Metabolites.dat Mon May 04 11:38:09 2020 -0400 @@ -1,27 +1,27 @@ -name formula charge -Suc C4H4O3 -1 -Fum C4H3O4 -1 -Mal C4H5O5 -1 -Cit C6H7O7 -1 -aKG C5H5O5 -1 -OA C4H3O5 -1 -Asp C4H6NO4 -1 -Aco C6HO3 -1 -2/3PG C3H6O3 -1 -G3P C3H7O3 -1 -PEP C3H4O3 -1 -E4P C4H8O4 -1 -R1P C5H8O4 -1 -R5P C5H8O4 -1 -G1P C6H10O5 -1 -G6P C6H10O5 -1 -F1P C6H10O5 -1 -F6P C6H10O5 -1 -M6P C6H10O5 -1 -6PG C6H10O6 -1 -S7P C7H11O6 -1 -FBP C6H11O8P -1 -AMP C10H14N5O4 -1 -ADP C10H14N5O4 -1 -ATP C10H16N5O10 -1 -CDP C9H15N3O7P -1 +name formula charge inchi +Suc C4H4O3 -1 InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)/p-2 +Fum C4H3O4 -1 InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/p-2/b2-1+ +Mal C4H5O5 -1 +Cit C6H7O7 -1 +aKG C5H5O5 -1 +OA C4H3O5 -1 +Asp C4H6NO4 -1 +Aco C6HO3 -1 +2/3PG C3H6O3 -1 +G3P C3H7O3 -1 +PEP C3H4O3 -1 +E4P C4H8O4 -1 +R1P C5H8O4 -1 +R5P C5H8O4 -1 +G1P C6H10O5 -1 +G6P C6H10O5 -1 +F1P C6H10O5 -1 +F6P C6H10O5 -1 +M6P C6H10O5 -1 +6PG C6H10O6 -1 +S7P C7H11O6 -1 +FBP C6H11O8P -1 +AMP C10H14N5O4 -1 +ADP C10H14N5O4 -1 +ATP C10H16N5O10 -1 +CDP C9H15N3O7P -1
--- a/test-data/results.log Mon May 27 03:33:36 2019 -0400 +++ b/test-data/results.log Mon May 04 11:38:09 2020 -0400 @@ -1,58 +1,59 @@ -2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ -2019-02-20 15:46:03 - root - INFO - Correction process -2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ -2019-02-20 15:46:03 - root - INFO - data files -2019-02-20 15:46:03 - root - INFO - data file: Data_example.tsv -2019-02-20 15:46:03 - root - INFO - derivatives database: Derivatives.dat -2019-02-20 15:46:03 - root - INFO - metabolites database: Metabolites.dat -2019-02-20 15:46:03 - root - INFO - isotopes database: Isotopes.dat -2019-02-20 15:46:03 - root - INFO - correction parameters -2019-02-20 15:46:03 - root - INFO - isotopic tracer: 13C -2019-02-20 15:46:03 - root - INFO - correct natural abundance of the tracer element: False -2019-02-20 15:46:03 - root - INFO - isotopic purity of the tracer: None -2019-02-20 15:46:03 - root - INFO - mode: low-resolution -2019-02-20 15:46:03 - root - INFO - natural abundance of isotopes -2019-02-20 15:46:03 - root - INFO - {'C': {'mass': [Decimal('12.0'), Decimal('13.003354835')], 'abundance': [0.9893, 0.0107]}, 'H': {'mass': [Decimal('1.0078250322'), Decimal('2.0141017781')], 'abundance': [0.999885, 0.000115]}, 'N': {'mass': [Decimal('14.003074004'), Decimal('15.000108899')], 'abundance': [0.99636, 0.00364]}, 'O': {'mass': [Decimal('15.99491462'), Decimal('16.999131757'), Decimal('17.999159613')], 'abundance': [0.99757, 0.00038, 0.00205]}, 'P': {'mass': [Decimal('30.973761998')], 'abundance': [1.0]}, 'S': {'mass': [Decimal('31.972071174'), Decimal('32.971458910'), Decimal('33.9678670'), Decimal('35'), Decimal('35.967081')], 'abundance': [0.9499, 0.0075, 0.0425, 0.0, 0.0001]}, 'Si': {'mass': [Decimal('27.976926535'), Decimal('28.976494665'), Decimal('29.9737701')], 'abundance': [0.92223, 0.04685, 0.03092]}} -2019-02-20 15:46:03 - root - INFO - IsoCor version: 2.1.0 -2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ -2019-02-20 15:46:03 - root - INFO - Constructing correctors for all (metabolite, derivative)... -2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ -2019-02-20 15:46:03 - root - INFO - ('Fum', '') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('OA', '') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('aKG', '') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('G3P', '') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('2/3PG', '') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('E4P', '') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('Fum', 'TMS') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('OA', 'TMS') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('aKG', 'TMS') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('G3P', 'TMS') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('2/3PG', 'TMS') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ('E4P', 'TMS') successfully constructed. -2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ -2019-02-20 15:46:03 - root - INFO - Correcting raw MS data... -2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ -2019-02-20 15:46:03 - root - INFO - Sample_1 - ('Fum', ''): processed -2019-02-20 15:46:03 - root - INFO - Sample_2 - ('Fum', ''): processed -2019-02-20 15:46:03 - root - INFO - Sample_1 - ('OA', ''): processed -2019-02-20 15:46:03 - root - INFO - Sample_2 - ('OA', ''): processed -2019-02-20 15:46:03 - root - INFO - Sample_1 - ('aKG', ''): processed -2019-02-20 15:46:03 - root - INFO - Sample_2 - ('aKG', ''): processed -2019-02-20 15:46:03 - root - INFO - Sample_1 - ('G3P', ''): processed -2019-02-20 15:46:04 - root - INFO - Sample_2 - ('G3P', ''): processed -2019-02-20 15:46:04 - root - INFO - Sample_1 - ('2/3PG', ''): processed -2019-02-20 15:46:04 - root - INFO - Sample_2 - ('2/3PG', ''): processed -2019-02-20 15:46:04 - root - INFO - Sample_1 - ('E4P', ''): processed -2019-02-20 15:46:04 - root - INFO - Sample_2 - ('E4P', ''): processed -2019-02-20 15:46:04 - root - INFO - Sample_3 - ('Fum', 'TMS'): processed -2019-02-20 15:46:04 - root - INFO - Sample_3 - ('OA', 'TMS'): processed -2019-02-20 15:46:04 - root - INFO - Sample_3 - ('aKG', 'TMS'): processed -2019-02-20 15:46:04 - root - INFO - Sample_3 - ('G3P', 'TMS'): processed -2019-02-20 15:46:04 - root - INFO - Sample_3 - ('2/3PG', 'TMS'): processed -2019-02-20 15:46:04 - root - INFO - Sample_3 - ('E4P', 'TMS'): processed -2019-02-20 15:46:04 - root - INFO - ------------------------------------------------ -2019-02-20 15:46:04 - root - INFO - Correction process summary -2019-02-20 15:46:04 - root - INFO - ------------------------------------------------ -2019-02-20 15:46:04 - root - INFO - number of samples: 3 -2019-02-20 15:46:04 - root - INFO - number of (metabolite, derivative): 12 -2019-02-20 15:46:04 - root - INFO - errors: 0 +2020-05-04 16:44:12 - numexpr.utils - INFO - NumExpr defaulting to 4 threads. +2020-05-04 16:44:12 - root - INFO - ------------------------------------------------ +2020-05-04 16:44:12 - root - INFO - Correction process +2020-05-04 16:44:12 - root - INFO - ------------------------------------------------ +2020-05-04 16:44:12 - root - INFO - data files +2020-05-04 16:44:12 - root - INFO - data file: Data_example.tsv +2020-05-04 16:44:12 - root - INFO - derivatives database: Derivatives.dat +2020-05-04 16:44:12 - root - INFO - metabolites database: Metabolites.dat +2020-05-04 16:44:12 - root - INFO - isotopes database: Isotopes.dat +2020-05-04 16:44:12 - root - INFO - correction parameters +2020-05-04 16:44:12 - root - INFO - isotopic tracer: 13C +2020-05-04 16:44:12 - root - INFO - correct natural abundance of the tracer element: False +2020-05-04 16:44:12 - root - INFO - isotopic purity of the tracer: None +2020-05-04 16:44:12 - root - INFO - mode: low-resolution +2020-05-04 16:44:12 - root - INFO - natural abundance of isotopes +2020-05-04 16:44:12 - root - INFO - {'C': {'mass': [Decimal('12.0'), Decimal('13.003354835')], 'abundance': [0.9893, 0.0107]}, 'H': {'mass': [Decimal('1.0078250322'), Decimal('2.0141017781')], 'abundance': [0.999885, 0.000115]}, 'N': {'mass': [Decimal('14.003074004'), Decimal('15.000108899')], 'abundance': [0.99636, 0.00364]}, 'O': {'mass': [Decimal('15.99491462'), Decimal('16.999131757'), Decimal('17.999159613')], 'abundance': [0.99757, 0.00038, 0.00205]}, 'P': {'mass': [Decimal('30.973761998')], 'abundance': [1.0]}, 'S': {'mass': [Decimal('31.972071174'), Decimal('32.971458910'), Decimal('33.9678670'), Decimal('35'), Decimal('35.967081')], 'abundance': [0.9499, 0.0075, 0.0425, 0.0, 0.0001]}, 'Si': {'mass': [Decimal('27.976926535'), Decimal('28.976494665'), Decimal('29.9737701')], 'abundance': [0.92223, 0.04685, 0.03092]}} +2020-05-04 16:44:12 - root - INFO - IsoCor version: 2.2.0 +2020-05-04 16:44:12 - root - INFO - ------------------------------------------------ +2020-05-04 16:44:12 - root - INFO - Constructing correctors for all (metabolite, derivative)... +2020-05-04 16:44:12 - root - INFO - ------------------------------------------------ +2020-05-04 16:44:12 - root - INFO - ('Fum', '') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('OA', '') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('aKG', '') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('G3P', '') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('2/3PG', '') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('E4P', '') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('Fum', 'TMS') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('OA', 'TMS') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('aKG', 'TMS') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('G3P', 'TMS') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('2/3PG', 'TMS') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ('E4P', 'TMS') successfully constructed. +2020-05-04 16:44:12 - root - INFO - ------------------------------------------------ +2020-05-04 16:44:12 - root - INFO - Correcting raw MS data... +2020-05-04 16:44:12 - root - INFO - ------------------------------------------------ +2020-05-04 16:44:12 - root - INFO - Sample_1 - ('Fum', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_2 - ('Fum', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_1 - ('OA', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_2 - ('OA', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_1 - ('aKG', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_2 - ('aKG', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_1 - ('G3P', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_2 - ('G3P', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_1 - ('2/3PG', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_2 - ('2/3PG', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_1 - ('E4P', ''): processed +2020-05-04 16:44:12 - root - INFO - Sample_2 - ('E4P', ''): processed +2020-05-04 16:44:13 - root - INFO - Sample_3 - ('Fum', 'TMS'): processed +2020-05-04 16:44:13 - root - INFO - Sample_3 - ('OA', 'TMS'): processed +2020-05-04 16:44:13 - root - INFO - Sample_3 - ('aKG', 'TMS'): processed +2020-05-04 16:44:13 - root - INFO - Sample_3 - ('G3P', 'TMS'): processed +2020-05-04 16:44:13 - root - INFO - Sample_3 - ('2/3PG', 'TMS'): processed +2020-05-04 16:44:13 - root - INFO - Sample_3 - ('E4P', 'TMS'): processed +2020-05-04 16:44:13 - root - INFO - ------------------------------------------------ +2020-05-04 16:44:13 - root - INFO - Correction process summary +2020-05-04 16:44:13 - root - INFO - ------------------------------------------------ +2020-05-04 16:44:13 - root - INFO - number of samples: 3 +2020-05-04 16:44:13 - root - INFO - number of (metabolite, derivative): 12 +2020-05-04 16:44:13 - root - INFO - errors: 0
--- a/test-data/results.tsv Mon May 27 03:33:36 2019 -0400 +++ b/test-data/results.tsv Mon May 04 11:38:09 2020 -0400 @@ -1,89 +1,89 @@ -sample metabolite derivative isotopologue area corrected_area isotopologue_fraction residuum mean_enrichment -Sample_1 Fum 0 376000.0 379808.0494972019 0.41168665351703776 0.0 0.2897659902799015 -Sample_1 Fum 1 235000.0 236670.2675765585 0.2565348221938963 0.0 0.2897659902799015 -Sample_1 Fum 2 127000.0 124721.39583086275 0.13518969421410323 1.5800125112233282e-17 0.2897659902799015 -Sample_1 Fum 3 143000.0 142264.79335165164 0.15420556980234792 -3.1600250224466564e-17 0.2897659902799015 -Sample_1 Fum 4 40000.0 39101.348751418525 0.04238326027261486 0.0 0.2897659902799015 -Sample_2 Fum 0 376000.0 379808.0494972019 0.41168665351703776 0.0 0.2897659902799015 -Sample_2 Fum 1 235000.0 236670.2675765585 0.2565348221938963 0.0 0.2897659902799015 -Sample_2 Fum 2 127000.0 124721.39583086275 0.13518969421410323 1.5800125112233282e-17 0.2897659902799015 -Sample_2 Fum 3 143000.0 142264.79335165164 0.15420556980234792 -3.1600250224466564e-17 0.2897659902799015 -Sample_2 Fum 4 40000.0 39101.348751418525 0.04238326027261486 0.0 0.2897659902799015 -Sample_1 OA 0 0.0 0.0 -Sample_1 OA 1 0.0 0.0 -Sample_1 OA 2 0.0 0.0 -Sample_1 OA 3 0.0 0.0 -Sample_1 OA 4 0.0 0.0 -Sample_2 OA 0 0.0 0.0 -Sample_2 OA 1 0.0 0.0 -Sample_2 OA 2 0.0 0.0 -Sample_2 OA 3 0.0 0.0 -Sample_2 OA 4 0.0 0.0 -Sample_1 aKG 0 761000.0 770757.2822531819 0.5971059382536738 -1.9986617443107176e-07 0.15239309254478398 -Sample_1 aKG 1 95100.0 94408.21105160222 0.07313807438059411 -1.1232997022303625e-07 0.15239309254478398 -Sample_1 aKG 2 391000.0 387815.2020768239 0.3004405737538707 3.24340113523371e-05 0.15239309254478398 -Sample_1 aKG 3 39300.0 37840.9710506128 0.029315413611861445 1.0996123584802932e-05 0.15239309254478398 -Sample_1 aKG 4 0.0 0.0 0.0 -0.003157788575981497 0.15239309254478398 -Sample_1 aKG 5 0.0 0.0 0.0 -0.00030802561931763875 0.15239309254478398 -Sample_2 aKG 0 761000.0 770757.2822531819 0.5971059382536738 -1.9986617443107176e-07 0.15239309254478398 -Sample_2 aKG 1 95100.0 94408.21105160222 0.07313807438059411 -1.1232997022303625e-07 0.15239309254478398 -Sample_2 aKG 2 391000.0 387815.2020768239 0.3004405737538707 3.24340113523371e-05 0.15239309254478398 -Sample_2 aKG 3 39300.0 37840.9710506128 0.029315413611861445 1.0996123584802932e-05 0.15239309254478398 -Sample_2 aKG 4 0.0 0.0 0.0 -0.003157788575981497 0.15239309254478398 -Sample_2 aKG 5 0.0 0.0 0.0 -0.00030802561931763875 0.15239309254478398 -Sample_1 G3P 0 715000.0 720817.843203928 0.5037179457196655 -8.142070347386684e-17 0.2307972956362909 -Sample_1 G3P 1 557000.0 560128.1627924398 0.3914256703849595 8.142070347386684e-17 0.2307972956362909 -Sample_1 G3P 2 24800.0 19465.731702013378 0.013602935162211748 -5.088793967116678e-17 0.2307972956362909 -Sample_1 G3P 3 133000.0 130583.22551280692 0.09125344873316321 1.2213105521080026e-16 0.2307972956362909 -Sample_2 G3P 0 715000.0 720817.843203928 0.5037179457196655 -8.142070347386684e-17 0.2307972956362909 -Sample_2 G3P 1 557000.0 560128.1627924398 0.3914256703849595 8.142070347386684e-17 0.2307972956362909 -Sample_2 G3P 2 24800.0 19465.731702013378 0.013602935162211748 -5.088793967116678e-17 0.2307972956362909 -Sample_2 G3P 3 133000.0 130583.22551280692 0.09125344873316321 1.2213105521080026e-16 0.2307972956362909 -Sample_1 2/3PG 0 1430000.0 1441469.8983039188 0.26951520374142846 0.0 0.350613297990272 -Sample_1 2/3PG 1 2920000.0 2940779.0438875123 0.5498447550687304 0.0 0.350613297990272 -Sample_1 2/3PG 2 226000.0 213534.01511096465 0.03992498466743767 1.0898270157923124e-17 0.350613297990272 -Sample_1 2/3PG 3 765000.0 752597.6842841837 0.1407150565224034 2.1796540315846248e-17 0.350613297990272 -Sample_2 2/3PG 0 1430000.0 1441469.8983039188 0.26951520374142846 0.0 0.350613297990272 -Sample_2 2/3PG 1 2920000.0 2940779.0438875123 0.5498447550687304 0.0 0.350613297990272 -Sample_2 2/3PG 2 226000.0 213534.01511096465 0.03992498466743767 1.0898270157923124e-17 0.350613297990272 -Sample_2 2/3PG 3 765000.0 752597.6842841837 0.1407150565224034 2.1796540315846248e-17 0.350613297990272 -Sample_1 E4P 0 854.0 863.1453281237473 0.041336917027350754 2.4329549962951284e-14 0.3817239095188967 -Sample_1 E4P 1 10200.0 10307.12055255345 0.4936185983859252 -1.0461978931437058e-14 0.3817239095188967 -Sample_1 E4P 2 7760.0 7810.814463659301 0.37406793373042024 1.508268629282176e-14 0.3817239095188967 -Sample_1 E4P 3 1730.0 1644.6719684418108 0.0787650311963941 -2.3299698911887947e-14 0.3817239095188967 -Sample_1 E4P 4 320.0 254.98554081254488 0.012211519659909676 3.423846073733581e-14 0.3817239095188967 -Sample_2 E4P 0 854.0 863.1453281237473 0.041336917027350754 2.4329549962951284e-14 0.3817239095188967 -Sample_2 E4P 1 10200.0 10307.12055255345 0.4936185983859252 -1.0461978931437058e-14 0.3817239095188967 -Sample_2 E4P 2 7760.0 7810.814463659301 0.37406793373042024 1.508268629282176e-14 0.3817239095188967 -Sample_2 E4P 3 1730.0 1644.6719684418108 0.0787650311963941 -2.3299698911887947e-14 0.3817239095188967 -Sample_2 E4P 4 320.0 254.98554081254488 0.012211519659909676 3.423846073733581e-14 0.3817239095188967 -Sample_3 Fum TMS 0 376000.0 425785.0538505561 0.45766573056460497 0.0 0.2626278340043467 -Sample_3 Fum TMS 1 235000.0 229433.5002431335 0.24661234478564592 -3.1600250224466564e-17 0.2626278340043467 -Sample_3 Fum TMS 2 127000.0 105318.33031467753 0.11320404544361702 -3.1600250224466564e-17 0.2626278340043467 -Sample_3 Fum TMS 3 143000.0 141951.9567793512 0.15258061648002147 3.1600250224466564e-17 0.2626278340043467 -Sample_3 Fum TMS 4 40000.0 27851.853810968023 0.029937262726110622 0.0 0.2626278340043467 -Sample_3 OA TMS 0 0.0 0.0 -Sample_3 OA TMS 1 0.0 0.0 -Sample_3 OA TMS 2 0.0 0.0 -Sample_3 OA TMS 3 0.0 0.0 -Sample_3 OA TMS 4 0.0 0.0 -Sample_3 aKG TMS 0 761000.0 864080.4383954712 0.6634102607174354 -1.4215099326884681e-05 0.1302868347875265 -Sample_3 aKG TMS 1 95100.0 33111.70372452174 0.02542198969516514 -7.027619573886684e-05 0.1302868347875265 -Sample_3 aKG TMS 2 391000.0 400501.8154913149 0.3074910645197312 0.0005087109208496222 0.1302868347875265 -Sample_3 aKG TMS 3 39300.0 4788.818975572151 0.003676685067668318 0.0011821047313132886 0.1302868347875265 -Sample_3 aKG TMS 4 0.0 0.0 0.0 -0.013225164964720594 0.1302868347875265 -Sample_3 aKG TMS 5 0.0 0.0 0.0 -0.000751685958158175 0.1302868347875265 -Sample_3 G3P TMS 0 715000.0 806222.8908729891 0.5421097940219233 0.0011462823123024992 0.20893939381005114 -Sample_3 G3P TMS 1 557000.0 555357.5466204376 0.37342621825203837 0.002864378095056404 0.20893939381005114 -Sample_3 G3P TMS 2 24800.0 0.0 0.0 -0.03321751751634703 0.20893939381005114 -Sample_3 G3P TMS 3 133000.0 125614.40709996362 0.08446398772603834 -2.6150701541736555e-12 0.20893939381005114 -Sample_3 2/3PG TMS 0 1430000.0 1613070.9343452677 0.2934931923774996 0.0004794245823734611 0.3239815179271314 -Sample_3 2/3PG TMS 1 2920000.0 3153601.731582657 0.5737879345430535 0.0011960645935207325 0.3239815179271314 -Sample_3 2/3PG TMS 2 226000.0 0.0 0.0 -0.01388900414166337 0.3239815179271314 -Sample_3 2/3PG TMS 3 765000.0 729437.5548178032 0.1327188730794469 1.6153633993476813e-12 0.3239815179271314 -Sample_3 E4P TMS 0 854.0 967.700772009107 0.046150526549923535 -2.9138586415226663e-06 0.3493645351728113 -Sample_3 E4P TMS 1 10200.0 11473.616488166983 0.5471871653687257 -1.4649378122356719e-05 0.3493645351728113 -Sample_3 E4P TMS 2 7760.0 7752.336450775334 0.369715948921533 0.00010602215694356356 0.3493645351728113 -Sample_3 E4P TMS 3 1730.0 774.7044932023791 0.036946359159817824 0.000251776357076686 0.3493645351728113 -Sample_3 E4P TMS 4 320.0 0.0 0.0 -0.002903094538807673 0.3493645351728113 +sample metabolite derivative isotopologue isotopic_inchi area corrected_area isotopologue_fraction residuum mean_enrichment +Sample_1 Fum 0 /a(C4+0) 376000.0 379808.0494972019 0.41168665351703776 0.0 0.2897659902799015 +Sample_1 Fum 1 /a(C1+1),(C3+0) 235000.0 236670.2675765585 0.2565348221938963 0.0 0.2897659902799015 +Sample_1 Fum 2 /a(C2+1),(C2+0) 127000.0 124721.39583086275 0.13518969421410323 1.5800125112233282e-17 0.2897659902799015 +Sample_1 Fum 3 /a(C3+1),(C1+0) 143000.0 142264.79335165164 0.15420556980234792 -3.1600250224466564e-17 0.2897659902799015 +Sample_1 Fum 4 /a(C4+1) 40000.0 39101.348751418525 0.04238326027261486 0.0 0.2897659902799015 +Sample_2 Fum 0 /a(C4+0) 376000.0 379808.0494972019 0.41168665351703776 0.0 0.2897659902799015 +Sample_2 Fum 1 /a(C1+1),(C3+0) 235000.0 236670.2675765585 0.2565348221938963 0.0 0.2897659902799015 +Sample_2 Fum 2 /a(C2+1),(C2+0) 127000.0 124721.39583086275 0.13518969421410323 1.5800125112233282e-17 0.2897659902799015 +Sample_2 Fum 3 /a(C3+1),(C1+0) 143000.0 142264.79335165164 0.15420556980234792 -3.1600250224466564e-17 0.2897659902799015 +Sample_2 Fum 4 /a(C4+1) 40000.0 39101.348751418525 0.04238326027261486 0.0 0.2897659902799015 +Sample_1 OA 0 /a(C4+0) 0.0 0.0 +Sample_1 OA 1 /a(C1+1),(C3+0) 0.0 0.0 +Sample_1 OA 2 /a(C2+1),(C2+0) 0.0 0.0 +Sample_1 OA 3 /a(C3+1),(C1+0) 0.0 0.0 +Sample_1 OA 4 /a(C4+1) 0.0 0.0 +Sample_2 OA 0 /a(C4+0) 0.0 0.0 +Sample_2 OA 1 /a(C1+1),(C3+0) 0.0 0.0 +Sample_2 OA 2 /a(C2+1),(C2+0) 0.0 0.0 +Sample_2 OA 3 /a(C3+1),(C1+0) 0.0 0.0 +Sample_2 OA 4 /a(C4+1) 0.0 0.0 +Sample_1 aKG 0 /a(C5+0) 761000.0 770757.2822531819 0.5971059382536738 -1.9986617443107176e-07 0.15239309254478398 +Sample_1 aKG 1 /a(C1+1),(C4+0) 95100.0 94408.21105160222 0.07313807438059411 -1.1232997022303625e-07 0.15239309254478398 +Sample_1 aKG 2 /a(C2+1),(C3+0) 391000.0 387815.2020768239 0.3004405737538707 3.24340113523371e-05 0.15239309254478398 +Sample_1 aKG 3 /a(C3+1),(C2+0) 39300.0 37840.9710506128 0.029315413611861445 1.0996123584802932e-05 0.15239309254478398 +Sample_1 aKG 4 /a(C4+1),(C1+0) 0.0 0.0 0.0 -0.003157788575981497 0.15239309254478398 +Sample_1 aKG 5 /a(C5+1) 0.0 0.0 0.0 -0.00030802561931763875 0.15239309254478398 +Sample_2 aKG 0 /a(C5+0) 761000.0 770757.2822531819 0.5971059382536738 -1.9986617443107176e-07 0.15239309254478398 +Sample_2 aKG 1 /a(C1+1),(C4+0) 95100.0 94408.21105160222 0.07313807438059411 -1.1232997022303625e-07 0.15239309254478398 +Sample_2 aKG 2 /a(C2+1),(C3+0) 391000.0 387815.2020768239 0.3004405737538707 3.24340113523371e-05 0.15239309254478398 +Sample_2 aKG 3 /a(C3+1),(C2+0) 39300.0 37840.9710506128 0.029315413611861445 1.0996123584802932e-05 0.15239309254478398 +Sample_2 aKG 4 /a(C4+1),(C1+0) 0.0 0.0 0.0 -0.003157788575981497 0.15239309254478398 +Sample_2 aKG 5 /a(C5+1) 0.0 0.0 0.0 -0.00030802561931763875 0.15239309254478398 +Sample_1 G3P 0 /a(C3+0) 715000.0 720817.843203928 0.5037179457196655 -8.142070347386684e-17 0.2307972956362909 +Sample_1 G3P 1 /a(C1+1),(C2+0) 557000.0 560128.1627924398 0.3914256703849595 8.142070347386684e-17 0.2307972956362909 +Sample_1 G3P 2 /a(C2+1),(C1+0) 24800.0 19465.731702013378 0.013602935162211748 -5.088793967116678e-17 0.2307972956362909 +Sample_1 G3P 3 /a(C3+1) 133000.0 130583.22551280692 0.09125344873316321 1.2213105521080026e-16 0.2307972956362909 +Sample_2 G3P 0 /a(C3+0) 715000.0 720817.843203928 0.5037179457196655 -8.142070347386684e-17 0.2307972956362909 +Sample_2 G3P 1 /a(C1+1),(C2+0) 557000.0 560128.1627924398 0.3914256703849595 8.142070347386684e-17 0.2307972956362909 +Sample_2 G3P 2 /a(C2+1),(C1+0) 24800.0 19465.731702013378 0.013602935162211748 -5.088793967116678e-17 0.2307972956362909 +Sample_2 G3P 3 /a(C3+1) 133000.0 130583.22551280692 0.09125344873316321 1.2213105521080026e-16 0.2307972956362909 +Sample_1 2/3PG 0 /a(C3+0) 1430000.0 1441469.8983039188 0.26951520374142846 0.0 0.350613297990272 +Sample_1 2/3PG 1 /a(C1+1),(C2+0) 2920000.0 2940779.0438875123 0.5498447550687304 0.0 0.350613297990272 +Sample_1 2/3PG 2 /a(C2+1),(C1+0) 226000.0 213534.01511096465 0.03992498466743767 1.0898270157923124e-17 0.350613297990272 +Sample_1 2/3PG 3 /a(C3+1) 765000.0 752597.6842841837 0.1407150565224034 2.1796540315846248e-17 0.350613297990272 +Sample_2 2/3PG 0 /a(C3+0) 1430000.0 1441469.8983039188 0.26951520374142846 0.0 0.350613297990272 +Sample_2 2/3PG 1 /a(C1+1),(C2+0) 2920000.0 2940779.0438875123 0.5498447550687304 0.0 0.350613297990272 +Sample_2 2/3PG 2 /a(C2+1),(C1+0) 226000.0 213534.01511096465 0.03992498466743767 1.0898270157923124e-17 0.350613297990272 +Sample_2 2/3PG 3 /a(C3+1) 765000.0 752597.6842841837 0.1407150565224034 2.1796540315846248e-17 0.350613297990272 +Sample_1 E4P 0 /a(C4+0) 854.0 863.1453281237473 0.041336917027350754 2.4329549962951284e-14 0.3817239095188967 +Sample_1 E4P 1 /a(C1+1),(C3+0) 10200.0 10307.12055255345 0.4936185983859252 -1.0461978931437058e-14 0.3817239095188967 +Sample_1 E4P 2 /a(C2+1),(C2+0) 7760.0 7810.814463659301 0.37406793373042024 1.508268629282176e-14 0.3817239095188967 +Sample_1 E4P 3 /a(C3+1),(C1+0) 1730.0 1644.6719684418108 0.0787650311963941 -2.3299698911887947e-14 0.3817239095188967 +Sample_1 E4P 4 /a(C4+1) 320.0 254.98554081254488 0.012211519659909676 3.423846073733581e-14 0.3817239095188967 +Sample_2 E4P 0 /a(C4+0) 854.0 863.1453281237473 0.041336917027350754 2.4329549962951284e-14 0.3817239095188967 +Sample_2 E4P 1 /a(C1+1),(C3+0) 10200.0 10307.12055255345 0.4936185983859252 -1.0461978931437058e-14 0.3817239095188967 +Sample_2 E4P 2 /a(C2+1),(C2+0) 7760.0 7810.814463659301 0.37406793373042024 1.508268629282176e-14 0.3817239095188967 +Sample_2 E4P 3 /a(C3+1),(C1+0) 1730.0 1644.6719684418108 0.0787650311963941 -2.3299698911887947e-14 0.3817239095188967 +Sample_2 E4P 4 /a(C4+1) 320.0 254.98554081254488 0.012211519659909676 3.423846073733581e-14 0.3817239095188967 +Sample_3 Fum TMS 0 /a(C4+0) 376000.0 425785.0538505561 0.45766573056460497 0.0 0.2626278340043467 +Sample_3 Fum TMS 1 /a(C1+1),(C3+0) 235000.0 229433.5002431335 0.24661234478564592 -3.1600250224466564e-17 0.2626278340043467 +Sample_3 Fum TMS 2 /a(C2+1),(C2+0) 127000.0 105318.33031467753 0.11320404544361702 -3.1600250224466564e-17 0.2626278340043467 +Sample_3 Fum TMS 3 /a(C3+1),(C1+0) 143000.0 141951.9567793512 0.15258061648002147 3.1600250224466564e-17 0.2626278340043467 +Sample_3 Fum TMS 4 /a(C4+1) 40000.0 27851.853810968023 0.029937262726110622 0.0 0.2626278340043467 +Sample_3 OA TMS 0 /a(C4+0) 0.0 0.0 +Sample_3 OA TMS 1 /a(C1+1),(C3+0) 0.0 0.0 +Sample_3 OA TMS 2 /a(C2+1),(C2+0) 0.0 0.0 +Sample_3 OA TMS 3 /a(C3+1),(C1+0) 0.0 0.0 +Sample_3 OA TMS 4 /a(C4+1) 0.0 0.0 +Sample_3 aKG TMS 0 /a(C5+0) 761000.0 864080.4383954712 0.6634102607174354 -1.4215099326884681e-05 0.1302868347875265 +Sample_3 aKG TMS 1 /a(C1+1),(C4+0) 95100.0 33111.70372452174 0.02542198969516514 -7.027619573886684e-05 0.1302868347875265 +Sample_3 aKG TMS 2 /a(C2+1),(C3+0) 391000.0 400501.8154913149 0.3074910645197312 0.0005087109208496222 0.1302868347875265 +Sample_3 aKG TMS 3 /a(C3+1),(C2+0) 39300.0 4788.818975572151 0.003676685067668318 0.0011821047313132886 0.1302868347875265 +Sample_3 aKG TMS 4 /a(C4+1),(C1+0) 0.0 0.0 0.0 -0.013225164964720594 0.1302868347875265 +Sample_3 aKG TMS 5 /a(C5+1) 0.0 0.0 0.0 -0.000751685958158175 0.1302868347875265 +Sample_3 G3P TMS 0 /a(C3+0) 715000.0 806222.8908729891 0.5421097940219233 0.0011462823123024992 0.20893939381005114 +Sample_3 G3P TMS 1 /a(C1+1),(C2+0) 557000.0 555357.5466204376 0.37342621825203837 0.002864378095056404 0.20893939381005114 +Sample_3 G3P TMS 2 /a(C2+1),(C1+0) 24800.0 0.0 0.0 -0.03321751751634703 0.20893939381005114 +Sample_3 G3P TMS 3 /a(C3+1) 133000.0 125614.40709996362 0.08446398772603834 -2.6150701541736555e-12 0.20893939381005114 +Sample_3 2/3PG TMS 0 /a(C3+0) 1430000.0 1613070.9343452677 0.2934931923774996 0.0004794245823734611 0.3239815179271314 +Sample_3 2/3PG TMS 1 /a(C1+1),(C2+0) 2920000.0 3153601.731582657 0.5737879345430535 0.0011960645935207325 0.3239815179271314 +Sample_3 2/3PG TMS 2 /a(C2+1),(C1+0) 226000.0 0.0 0.0 -0.01388900414166337 0.3239815179271314 +Sample_3 2/3PG TMS 3 /a(C3+1) 765000.0 729437.5548178032 0.1327188730794469 1.6153633993476813e-12 0.3239815179271314 +Sample_3 E4P TMS 0 /a(C4+0) 854.0 967.700772009107 0.046150526549923535 -2.9138586415226663e-06 0.3493645351728113 +Sample_3 E4P TMS 1 /a(C1+1),(C3+0) 10200.0 11473.616488166983 0.5471871653687257 -1.4649378122356719e-05 0.3493645351728113 +Sample_3 E4P TMS 2 /a(C2+1),(C2+0) 7760.0 7752.336450775334 0.369715948921533 0.00010602215694356356 0.3493645351728113 +Sample_3 E4P TMS 3 /a(C3+1),(C1+0) 1730.0 774.7044932023791 0.036946359159817824 0.000251776357076686 0.3493645351728113 +Sample_3 E4P TMS 4 /a(C4+1) 320.0 0.0 0.0 -0.002903094538807673 0.3493645351728113