CycloBranch: Tutorials

Tutorial 1: Dereplication in MS1 data
Tutorial 2: Dereplication in LC-MS data
Tutorial 3: Identification of unknown compounds in LC-MS data
Tutorial 4: Dereplication in MSI data and fusion with histology image
Tutorial 5: Identification of unknown compounds in MSI data
Tutorial 6: Annotate MS/MS spectrum of a metabolite
MassSpecBlocks: Tutorial, Homepage, Reference and more information

If you would like to annotate single MS/MS spectra of (non-)ribosomal peptides and siderophores, see the tutorials for CycloBranch (1.x). See also the extra pages for linear, cyclic, branched, and branch-cyclic peptides; the building blocks editor, sequence/compound database editor, modifications editor, and draw peptide tool.

Tutorials (CycloBranch 1.x)

Tutorial 1: Does a peptide have a cycle ?
Tutorial 2: How to determine a tag ?
Tutorial 3: How to determine a complete sequence ?
Tutorial 4: How to determine a branched sequence ?
Tutorial 5: How to determine terminal modifications ?
Tutorial 6: How to compare a theoretical spectrum with a peaklist ?
Tutorial 7: How to search in a database of MS/MS spectra ?
Tutorial 8: How to search MS spectrum against a database of compounds ?
Tutorial 9: Draw Peptide Tool
Tutorial 10: Identification of Branch-Cyclic Peptide with a Long-sized Branch
Tutorial 11: Identification of Peptide Family using Similarity Search
Tutorial 12: Identification of Siderophores in MS/MS data
Tutorial 13: Identification of Siderophores in MALDI-MS and LC-MS data
Tutorial 14: Identification of Siderophores in Imaging Mass Spectra

See also a recent protocol on how to configure CycloBranch for different use-cases:

Tomas Pluhacek, Anton Skriba, Jiri Novak, Dominika Luptakova and Vladimir Havlicek.
Analysis of Microbial Siderophores by Mass Spectrometry.
In: Sanjoy K. Bhattacharya (ed.), Metabolomics: Methods and Protocols, Methods in Molecular Biology, vol. 1996, pp. 131-153, Springer, 2019. DOI: 10.1007/978-1-4939-9488-5_12.