DOI: 10.5281/zenodo.11126499
title: Supporting information data on silylated metabolites

description: There are theoretical quantum chemical data (output files) of computations of mass spectrometric parent and product ions of metabolomics compounds depending on theoretical levels in ground and transition states, in addition to chemometrics.

There are used the following abbreviations:

Quantum chemical data:

2OHMA - 2-hydroxy-3-methylbutyric acid 3MGA - 3-methylglutaric acidApi - ApigeninBenz76 - Phenyl-fragment cation at m/z 76BOMD - Born–Oppenheimer molecular dynamicsFA - Fumaric acidFa-425.opj - Visualized molecular mechanics - molecular dynamics data on fumaric acid cation at m/z 245 in it cis-, respectively, trans configurations.Apigenine-QQ.opj - Visualized M062X/SDD molecular optimization of apigenin and genistein cations at m/z 242.   Freq - frequency analysisGenis - GenisteinGS - Ground stateMD - molecular dynamicsMM2 - Molecular mechanicsOA - Oxalic acidOpt - Optimization of speciesPy76- Pyridinium ion at m/z 76Si - Data on silicon containing ions TFAA - Trifluoroacetic acid and its derivativesTMS - TrimethylsilylTS - Transition state

Born–Oppenheimer molecular dynamics are shown as txt files, as well as, containing tabulated:

# X-Axis:  Time in Trajectory (femtosec)# Y-Axis:  Potential Energy (Hartree)

data on the computed species.The same is valid to data on molecular optimization given as tables containing:

# X-Axis:  Optimization Step Number# Y-Axis:  Total Energy (Hartree).

The txt-files files contain extracted parameters from the corresponding output files of quantum chemical computations.

For instance, file:Fa-245-b-trans.out, meanstheoretical data on fumaric acid derivative cation at m/z 245 in its trans-configuration and type "b".

Chemometrics:Tabulated mass spectrometric data on oxalic, arabinoic, glyceric, malonic, glycolic and fumaric acids derivatives as well as chemomerics.There are also data on apigenin.

Arabinoicacid.opj Apigenine.opj FA-QQ.opjFA-MS.opjGlyceric acid.opjGlycolic acid.opjMalonic acid.opjOA-MS.opj

FA_MS.opj(Mass spectrometric data on metabolite at RT=14.29 min and spectra of standard samples of fumaric acid (FA) E and Z isomer from databases DB1-DB4 as well as theoretical intensity data on equation (6) of parent and fragment ions of fumaric acid.)FAmz - Examined m/z ions.AnalRT1429 - experimental r.i. % data on metabolite at RT=14.29 min.FADB1 - Experimental r.i. % data on standard sample of fumaric acid according to DB1.FADB3 - Experimental r.i. % data on standard sample of fumaric acid according to DB3.FAEDB2 - Experimental r.i. % data on standard sample of E isomer of fumaric acid according to DB2.FAZDB3 - Experimental r.i. % data on standard sample of Z isomer of fumaric acid according to DB2.Ither, Itheor1, Itheorpy - theoretical intensity data on equation (6) of ions of fumaric acid accounting fordifferent type of 3D molecular and electronic structures of species; peak at m/z 76 is exmined assessing pyridinium cation and benzene cation-radical (data on Table 1 in the contribution.)  

FA_MS.opj(Mass spectrometric data on metabolite at RT=18.26 min and spectra of standard samples of oxalic acid (OA), succinic acid (SA), and 2-hydroxy-3-methylbutyric acid (2OHMA) from databases DB1-DB4 as well as theoretical intensity data on equation (6) of parent and fragment ions of the acids.)mz - Examined m/z ions.AnalRT1826 - Experimental r.i. % data on metabolite at RT=18.26 min. OADB1 - Experimental r.i. % data on standard sample of oxalic acid according to DB1. OADB2 - Experimental r.i. % data on standard sample of oxalic acid according to DB2. OADB4 - Experimental r.i. % data on standard sample of oxalic acid according to DB4. SUAREF30- Experimental r.i. % data on standard sample of succinic acid according to reference [30]. [30] Hecht, H.; Trojak, M. Galaxy training material for mass spectrometry: GC–MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) [Data set]. Zenodo. CERN Data Centre repository, 2023. [https://doi.org/10.5281/zenodo.7890956] (created May 3, 2023.) 2OHMADB2 - Experimental r.i. % data on standard sample of 2-hydroxy-3-methylbutyric acid 2TMS according to DB2.  2OHMA2DB2 - Experimental r.i. % data on standard sample of 2-hydroxy-3-methylbutyric acid 2TBDMS according to DB2. ItherSDOA, Itheor2OHMA - theoretical intensity data on equation (6) of ions of oxalic acid and 2-hydroxy-3-methylbutyric acid accounting fordifferent type of 3D molecular and electronic structures of species (data on Table 1 in the contribution.)   2OHMA331opt - DFT optimization of mass spectrometric species of 2-hydroxy-3-methylbutyric acid of ion at m/z 331.

DB2: Oxalic acid, 2TMS derivative, [https://webbook.nist.gov/cgi/inchi?ID=C18294047&Mask=200]; butanedioic acid (succinic acid), 2TMS derivative, [https://webbook.nist.gov/cgi/inchi?ID=C40309577&Mask=200]; glyceric acid, 3TMS derivative, [https://webbook.nist.gov/cgi/inchi?ID=C38191876&Mask=200]; propanedioic acid (malonic acid), 2TMS derivative, [https://webbook.nist.gov/cgi/inchi?ID=C18457040&Mask=200]; 2-butenedioic acid (fumaric acid), (E)-, 2TMS derivative, [https://webbook.nist.gov/cgi/inchi?ID=C17962037&Mask=200]; 2-butenedioic acid (fumaric acid), (Z)-, 2TMS derivative,  [https://webbook.nist.gov/cgi/inchi?ID=C23508829&Mask=200], 2-hydroxy-3-methylbutyric acid, 2TMS derivative [https://webbook.nist.gov/cgi/inchi?ID=C55124920&Mask=200], and butanoic acid, 2-[(tert-butyldimethylsilyl)oxy]-3-methyl-, tert-butyldimethylsilyl ester (2-hydroxy-3-methylbutyric acid, 2TBDMS derivative [https://webbook.nist.gov/cgi/cbook.cgi?ID=C180784672&Mask=200],) respectively.DB3: Reference [4].DB4: For metabolite annotation, there has been employed Kovats RI library containing EI-MS spectra as well [32].[4] Price, E.; Coufalíkova, K.; Jbebli, A.; Palat, J.; Koudelka, S.; Klanova, J. RECETOX Metabolome HR-[EI+]-MS library (1.0.0) [Data set]. Zenodo, CERN Data Centre repository, 2021; [https://doi.org/10.5281/zenodo.5483565].[32] Kovats RI library of EI-MS spectra of standard samples, RIKEN Center for Sustainable Resource Science, Yokohama, Japan [http://prime.psc.riken.jp/compms/msdial/main.html#MSP] (created June 29, 2007.)

Files *.out and *.txt can be viewed via Editor.Files *.opj can be viewed via Originviewer. It can be downloaded free of charge:

[https://www.originlab.com/viewer/].