Merge pull request #5710 from KristinaGomoryova/mfassignr-tutorial

Galaxy training for the MFAssignR tool

Author: hechth

CONTRIBUTORS.yaml

@@ -2621,6 +2621,10 @@ sitjart:
     affiliations:
       - elixir-europe
 
+skschum:
+    name: Simeon Schum
+    joined: 2025-02
+
 slegras:
     name: Stéphanie Legras
     joined: 2017-09

topics/metabolomics/tutorials/mfassignr/data-library.yaml

@@ -0,0 +1,19 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: The new topic
+  description: Summary
+  items:
+  - name: Molecular formula assignment and recalibration with MFAssignR package
+    items:
+    - name: 'DOI: 10.5281/zenodo.13768009'
+      description: latest
+      items:
+      - url: https://zenodo.org/records/13768009/files/mfassignr_input.txt
+        src: url
+        ext: auto
+        info: https://zenodo.org/records/13768009

topics/metabolomics/tutorials/mfassignr/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/metabolomics/tutorials/mfassignr/images/KMDplot.png

@@ -0,0 +1,114 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Schum2020,
+  title = {MFAssignR: Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures},
+  volume = {191},
+  ISSN = {0013-9351},
+  url = {http://dx.doi.org/10.1016/j.envres.2020.110114},
+  DOI = {10.1016/j.envres.2020.110114},
+  journal = {Environmental Research},
+  publisher = {Elsevier BV},
+  author = {Schum,  Simeon K. and Brown,  Laura E. and Mazzoleni,  Lynn R.},
+  year = {2020},
+  month = dec,
+  pages = {110114}
+}
+
+@article{Zheng2019,
+  title = {Resolution-enhanced Kendrick mass defect plots for the data processing of mass spectra from wood and coal hydrothermal extracts},
+  volume = {235},
+  ISSN = {0016-2361},
+  url = {http://dx.doi.org/10.1016/j.fuel.2018.08.085},
+  DOI = {10.1016/j.fuel.2018.08.085},
+  journal = {Fuel},
+  publisher = {Elsevier BV},
+  author = {Zheng,  Qingxin and Morimoto,  Masato and Sato,  Hiroaki and Fouquet,  Thierry},
+  year = {2019},
+  month = jan,
+  pages = {944–953}
+}
+
+@article{Kozhinov2013,
+  title = {Iterative Method for Mass Spectra Recalibration via Empirical Estimation of the Mass Calibration Function for Fourier Transform Mass Spectrometry-Based Petroleomics},
+  volume = {85},
+  ISSN = {1520-6882},
+  url = {http://dx.doi.org/10.1021/ac400972y},
+  DOI = {10.1021/ac400972y},
+  number = {13},
+  journal = {Analytical Chemistry},
+  publisher = {American Chemical Society (ACS)},
+  author = {Kozhinov,  Anton N. and Zhurov,  Konstantin O. and Tsybin,  Yury O.},
+  year = {2013},
+  month = jun,
+  pages = {6437–6445}
+}
+
+@article{Savory2011,
+  title = {Parts-Per-Billion Fourier Transform Ion Cyclotron Resonance Mass Measurement Accuracy with a “Walking” Calibration Equation},
+  volume = {83},
+  ISSN = {1520-6882},
+  url = {http://dx.doi.org/10.1021/ac102943z},
+  DOI = {10.1021/ac102943z},
+  number = {5},
+  journal = {Analytical Chemistry},
+  publisher = {American Chemical Society (ACS)},
+  author = {Savory,  Joshua J. and Kaiser,  Nathan K. and McKenna,  Amy M. and Xian,  Feng and Blakney,  Greg T. and Rodgers,  Ryan P. and Hendrickson,  Christopher L. and Marshall,  Alan G.},
+  year = {2011},
+  month = jan,
+  pages = {1732–1736}
+}
+
+@article{Green2015,
+  title = {Fast Graphically Inspired Algorithm for Assignment of Molecular Formulae in Ultrahigh Resolution Mass Spectrometry},
+  volume = {87},
+  ISSN = {1520-6882},
+  url = {http://dx.doi.org/10.1021/ac504166t},
+  DOI = {10.1021/ac504166t},
+  number = {10},
+  journal = {Analytical Chemistry},
+  publisher = {American Chemical Society (ACS)},
+  author = {Green,  Nelson W. and Perdue,  E. Michael},
+  year = {2015},
+  month = apr,
+  pages = {5086–5094}
+}
+
+@article{krevelen1950graphical,
+  title={Graphical-statistical method for the study of structure and reaction processes of coal.},
+  author={KREVELEN, VAN},
+  journal={Fuel},
+  volume={29},
+  pages={269--284},
+  year={1950},
+  url={https://api.semanticscholar.org/CorpusID:208705483}
+}
+
+@misc{kendrickmass_mzmine,
+    title = {4D features plot (Kendrick mass plot)},
+    url = {https://mzmine.github.io/mzmine_documentation/visualization_modules/kendrickmass/kendrick_mass_plot.html},
+    author = {mzmine},
+    year = {2024},
+    note = {Accessed on September 30, 2024}
+}
+
+@misc{kendrickmass_wiki,
+    title = {Kendrick mass},
+    url = {https://en.wikipedia.org/wiki/Kendrick_mass},
+    author = {wikipedia},
+    year = {2024},
+    note = {Accessed on September 30, 2024}
+}