IsotopoMatch - database of isotopic pattern
Creators: name: Erny, Guillaume
Publisher: name: Zenodo
Year: 2022
Subjects: Isotopic patterns

description: <strong>COPYRIGHT</strong><br> Copyright BSD 3-Clause License Copyright 2022 G. Erny (guillaume@fe.up.pt), FEUP, Porto, Portugal<br> Copyright 2022 G. Erny (guillaume@fe.up.pt)<br> Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:<br> Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.<br> Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.<br> Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.<br> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. <strong>ACKNOWLEDGEMENTS</strong><br> This work was financially supported by: (i) Base Funding—UIDB/00511/2020 of the Laboratory for Process Engineering, Environment, Biotechnology and Energy—LEPABE—funded by national funds through the FCT/MCTES (PIDDAC); (ii) Project POCI-01-0145-FEDER-029702, funded by FEDER funds through COMPETE2020—Programa Operacional Competitividade e Internacionalização (POCI) and by national funds (PIDDAC) through FCT/MCTES. <strong>INSTRUCTIONS</strong><br> <em>Introduction</em><br> The live script can be used to build a personalised database of isotopic patterns using ChemCalc [1] of ions generated during electrospray ionisation and detected by positive polarity. The live script needs a table of molecular formulas that is called ListMotif, with (at least) two columns. One column should be called Motif and is a cell array of character vectors that are the molecular formula respecting the Hill system order. The second one should be called Parsed_Motif, and are the formal representation of the molecular formulas obtained using the Matlab toolbox Stoich Tools [2]. This toolbox is also used in the live script and should be downloaded and installed in your Matlab path. The live script will build all possible adducts based on those formulas and obtain the isotopic patterns from ChemCal. An example of a ListMotif table can be obtained using <br> load('exmpleMotif.mat') <em>Adduct Structures </em><br> Adducts are built using the following structure:<br> Adduct = mM + N +Z<br> M is the original molecular formulae, m is the repetition of this motif, N is a neutral gain or loss and Z is the ionic termination. A list of possible builds can easily be found online. In the scripts, m is initialized line 91; the list of neutral gain/loss starts at line 11; and the list of terminations line 69. In this script, ESI+ ions were generated with a possible charge of 1 and 2, and a repetition of motif of 1 or 2. It should be emphasised that considering ions of charge 3 will drastically increase the size of the output database and should only be done with a small number of molecular formulas. <em>Output</em><br> The output of the script is a table, called myDataBase, with 6 columns: accession, the accession code (could be personalised line 204); mf, the molecular formulas of the adducts, monoisotopicMass, the monoisotopic mass calculated by ChemCalc; baseIonMass, the m/z value of the most intense peak in the isotopic pattern; IsotopicPattern, a m*2 array with, in first column the m/z value, and in second column the corresponding relative intensities; and AdductStructure, the list of all build leading to this formula. AdductStructure is only indicative.<br> <strong>HMDBv4_ESIplus</strong><br> HMDBv4_ESIplus is a database of ionic patterns obtained using the metabolomic database (v4) from the Human Metabolome Database (HMDB) [3]. In can be downloaded using<br> load('HMDBv4_ESIplus.mat')<br> The actual database is the field myDataBase in the HMDBv4_ESIplus structure. The database has been created using the following parameters: <br> m: 1 or 2<br> N: ''; '-H2O'; '+C2H7N'; '+C2H7N-H2O'; '+C2H3N'; '+C2H3N-H2O'; '+CH3O'; '+CH3O-H2O'; '+C3H8O'; '+C3H8O-H2O'; '+C2H6OS'; '-2H2O';<br> Z: Q = +1: '+H(+)'; '+Na(+)'; '+NH4(+)';<br> Q = +2: '+2H(+)'; '+2Na(+)'; '+2NH4(+)'; '+H(+)+Na(+)'; '+H(+)+NH4(+)'; '+Na(+)+NH4(+)'; <strong>REFERENCES</strong><br> [1] Patiny, L.; Borel, A (2013) ChemCalc: a building block for tomorrow’s chemical infrastructure. Journal of Chemical Information and Modeling, 53, 5, 1223–1228. DOI:10.1021/ci300563h<br> [2] Jeffrey K (2022). Stoichiometry Tools (https://www.mathworks.com/matlabcentral/fileexchange/29774-stoichiometry-tools), MATLAB Central File Exchange. Retrieved April 7, 2022.<br> [3] Wishart, D.S.; Feunang, Y.D:; Marcu, A.; Gua, A.C.; Liang, K., et al. (2018) HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Research. 46(D1):D608-D617. DOI: 10.1093/nar/gkx1089.