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Shunyang2018 / plot_msms_accurate

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Valine formulas all wrong #1

Closed tobigithub closed 3 years ago

tobigithub commented 3 years ago

Hi, I attached the input res file for valine case. The problem is that many of the formula annotations in accuratemass.jdx are wrong, hence all the output in my MSP file is also wrong.

For example H12C5N= 86.0969692 Da, but if I look into the accuratemass.jdx

##TITLE=Theoretical in-silico spectrum (QCEIMS)
##JCAMP-DX=4.24
##DATA TYPE=MASS SPECTRUM
##XUNITS=M/Z
##YUNITS=RELATIVE INTENSITY
##NPOINTS=21
##PEAK TABLE=(XY..XY) 1
18.034374           24.13  "H4N1"
29.013973           24.02  "H1N2"
43.054775           58.57  "H7C3"
44.058128            1.89  "H7C3"
58.065674           23.37  "H8C3N1"
72.081322           69.33  "H10C4N"
73.084679            2.95  "H10C4N"
73.089149          184.77  "H11C4N"
74.092506            7.78  "H11C4N"
100.076233          45.63  "H10C5N"
101.060257         137.05  "H9C5O2"
101.079590           2.37  "H10C5N"
102.063614           7.26  "H9C5O2"
118.086807        1000.00  "H12C5N"
119.083847           3.69  "H12C5N"
119.090164          53.74  "H12C5N"
119.093079           1.36  "H12C5N"
120.091049           4.16  "H12C5N"
120.093521           1.34  "H12C5N"
129.066406          68.03  "H9C5N2"
130.069763           3.61  "H9C5N2"
##END=

Five lines have false formulas, and the are completely off, because 118 Da is not 86 Da. 118.086807 1000.00 "H12C5N" 119.083847 3.69 "H12C5N" 119.090164 53.74 "H12C5N" 119.093079 1.36 "H12C5N" 120.091049 4.16 "H12C5N" 120.093521 1.34 "H12C5N"

Another case, H11C4N = 73.0891446 Da, hence it can not be m/z 74 or it has to be something else : 74.092506 7.78 "H11C4N"

Please correct these issues. Attached the res and jdx files (please rename back from TXT due to upload issues). We want to model accurate mass spectrometry, hence different m/z values can not be related to the same formula. Also we want accurate masses, not estimated or rounded masses. T. formula.txt qceims.res.txt accuratemass.jdx.txt

Shunyang2018 commented 3 years ago

Interesting. I will take a look tonight. But the H11C4N could be 74 because of the isotope C13. You can see the ratio between 73 and 74 is 184:7, consistent with isotope peak ratio with C4N 100:4.

tobigithub commented 3 years ago

Interesting. I will take a look tonight. But the H11C4N could be 74 because of the isotope C13. You can see the ratio between 73 and 74 is 184:7, consistent with isotope peak ratio with C4N 100:4.

True, but the peak annotations have to resolve to the correct elements, not sure how to solve that, maybe include the information thats an isotope peak (iso). Because m/z 74 would be H12C4N or designated [H11C4N] (M+1)

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tobigithub commented 3 years ago

So at the bare minimum, this is a handcurated(!) spectrum from the res file. This is the required manual validation it takes, its minimum because it has not isotope peak information. The count column is just for the EXCEL analysis and can be ignored. But this is what I want at minimum. This is correct as long as the frag program calculates the charges correctly.

Mass            Abund   Count   Formula
18.0343724  22.73   2   H4N1
29.0139726  22.73   2   H1N2
43.0547722  56.82   5   C3H7
58.0656708  22.73   2   C3H8N1
72.08132    68.18   6   C4H10N1
73.0891446  181.82  16  C4H11N1
100.076235  45.45   4   C5H10N1O1
101.0602514 136.36  12  C5H9O2
118.0867992 1000.00 88  C5H12N1O2
129.0663994 68.18   6   C5H9N2O2

Attached is the XLS file with the individual drill-down. Please download and look at it. qceimsres-analysis.xlsx

And the formatted file I create with a Python program:

Name: Valine (in-silico)
Precursor_type: [M+H]+
Spectrum_type: MS2
PrecursorMZ: 118.0863
Ion_mode: P
InChIKey: KZSNJWFQEVHDMF-UHFFFAOYSA-N
Formula: C5H11NO2
Comments: protomer of valine [M+H]+
NumPeaks: 11
18.0343724  22.73       "H4N1"
29.0139726  22.73       "H1N2"
43.0547722  56.82       "C3H7"
58.0656708  22.73       "C3H8N1"
72.08132    68.18       "C4H10N1"
73.0891446  181.82      "C4H11N1"
100.076235  45.45       "C5H10N1O1"
101.0602514 136.36      "C5H9O2"
118.0867992 1000.00     "C5H12N1O2"
129.0663994 68.18       "C5H9N2O2"

So the peaks match to the original, just the isotope peak formulas are not annotated correctly. They need to be marked with (iso) or otherwise. It like the isotope information, but for all the isotope peaks the annotations need to be changed (if possible), or left out.

Shunyang2018 commented 3 years ago

Hi, the wrong formula comes from the rigid length of the parameter. I change the length from 6 to 80 to show the full formula. I also add the * to show the isotope peak formula.

##TITLE=Theoretical in-silico spectrum (QCEIMS)
##JCAMP-DX=4.24
##DATA TYPE=MASS SPECTRUM
##XUNITS=M/Z
##YUNITS=RELATIVE INTENSITY
##NPOINTS=21
##PEAK TABLE=(XY..XY) 1
18.034374           24.10  "H4N1"
29.013973           24.02  "H1N2"
43.054775           58.50  "H7C3"
44.058128            1.94  "H7C3"                *
58.065674           23.32  "H8C3N1"
72.081322           69.33  "H10C4N1"
73.084679            2.91  "H10C4N1"             *
73.089149          184.85  "H11C4N1"
74.092506            7.71  "H11C4N1"             *
100.076233          45.61  "H10C5N1O1"
101.060257         136.99  "H9C5O2"
101.079590           2.39  "H10C5N1O1"
102.063614           7.32  "H9C5O2"
118.086807        1000.00  "H12C5N1O2"
119.083847           3.64  "H12C5N1O2"           *
119.090164          53.19  "H12C5N1O2"           *
119.093079           1.45  "H12C5N1O2"           *
120.091049           4.22  "H12C5N1O2"           *
120.093521           1.26  "H12C5N1O2"           *
129.066406          67.96  "H9C5N2O2"
130.069763           3.63  "H9C5N2O2"            *
##END=
tobigithub commented 3 years ago

Hi, the star or better (iso) annotation has to go into the brackets please: "H12C5N1O2 (iso)" otherwise the import does not work! Thanks!! T.

Dr. Tobias Kind UC Davis Genome Center Metabolomics

From: Shunyang2018 notifications@github.com Sent: Wednesday, January 6, 2021 2:06:30 PM To: Shunyang2018/plot_msms plot_msms@noreply.github.com Cc: Tobias Kind tkind@ucdavis.edu; Author author@noreply.github.com Subject: Re: [Shunyang2018/plot_msms] Valine formulas all wrong (#1)

Hi, the wrong formula comes from the rigid length of the parameter. I change the length from 6 to 80 to show the full formula. I also add the * to show the isotope peak formula.

TITLE=Theoretical in-silico spectrum (QCEIMS) ##JCAMP-DX=4.24 ##DATA TYPE=MASS SPECTRUM ##XUNITS=M/Z ##YUNITS=RELATIVE INTENSITY ##NPOINTS=21 ##PEAK TABLE=(XY..XY) 1 18.034374 24.10 "H4N1" 29.013973 24.02 "H1N2" 43.054775 58.50 "H7C3" 44.058128 1.94 "H7C3" 58.065674 23.32 "H8C3N1" 72.081322 69.33 "H10C4N1" 73.084679 2.91 "H10C4N1" 73.089149 184.85 "H11C4N1" 74.092506 7.71 "H11C4N1" 100.076233 45.61 "H10C5N1O1" 101.060257 136.99 "H9C5O2" 101.079590 2.39 "H10C5N1O1" 102.063614 7.32 "H9C5O2" 118.086807 1000.00 "H12C5N1O2" 119.083847 3.64 "H12C5N1O2" 119.090164 53.19 "H12C5N1O2" 119.093079 1.45 "H12C5N1O2" 120.091049 4.22 "H12C5N1O2" 120.093521 1.26 "H12C5N1O2" 129.066406 67.96 "H9C5N2O2" 130.069763 3.63 "H9C5N2O2" * ##END=

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Shunyang2018 commented 3 years ago

Please check this time. I prefer the "H12C5N1O2*" rather than "H12C5N1O2 (iso)". iso could also be iso-leucine, so I think a symbol is better. If you want I can change it.

tobigithub commented 3 years ago

Please change it to my preference. A star designates radicals, formulas dont have any isomer information, such as iso leucine. Therefore iso can only denote isotopes. Thanks T.

Dr. Tobias Kind UC Davis Genome Center Metabolomics

From: Shunyang2018 notifications@github.com Sent: Wednesday, January 6, 2021 2:23:17 PM To: Shunyang2018/plot_msms plot_msms@noreply.github.com Cc: Tobias Kind tkind@ucdavis.edu; Author author@noreply.github.com Subject: Re: [Shunyang2018/plot_msms] Valine formulas all wrong (#1)

Please check this time. I prefer the "H12C5N1O2*" rather than "H12C5N1O2 (iso)". iso could also be iso-leucine, so I think a symbol is better. If you want I can change it.

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Shunyang2018 commented 3 years ago

should work now.

tobigithub commented 3 years ago

Thank you! T.

Dr. Tobias Kind UC Davis Genome Center Metabolomics

From: Shunyang2018 notifications@github.com Sent: Wednesday, January 6, 2021 2:33:04 PM To: Shunyang2018/plot_msms plot_msms@noreply.github.com Cc: Tobias Kind tkind@ucdavis.edu; Author author@noreply.github.com Subject: Re: [Shunyang2018/plot_msms] Valine formulas all wrong (#1)

should work now.

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