martenson/recetox-xmsannotator

This is a custom adaptation of the original version of xMSannotator. It is a complete rewrite of the original functionality, following the same program structure.

xMSannotator

Built Docker images are available at recetox/xmsannotator.

Use as a Galaxy Tool: https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator

When using this tool, please cite the original publication.

Research reproducibility

Follows the list of information that is retrieved from online sources, therefore, they may cause issues regarding research reproducibility.

• compounds with HMDB IDs HMDB29244, HMDB29245, and HMDB29246 are excluded from pathway evaluation (annotation of unannotated features which are part of some pathway that is present in the analyzed sample).
  • possible explanation: these compounds are very similar and they probably cause errors since they are non-specifically related to various pathways (very late stage biosynthesis)
  • primary affected functions: multilevelannotationstep3
  • transitively affected functions: multilevelannotation
• attributes BRITE, PATHWAYS, and DBLINKS are retrieved from online KEGG database
  • conditionally (defaults to not to) the HMDB ID and LipidMaps ID are extracted from DBLINKS if present
  • implications: since these are not important attributes and are added to the result just for convenience, the annotation algorithm is unaffected
  • primary affected functions: Annotationbychemical_IDschild, Annotationbychemical_IDschildsimple, Annotationbychemical_IDschild_multilevel
  • transitively affected functions: simpleAnnotation, multilevelannotation, Annotationbychemical_IDs
• attributes FORMULA, NAME, and EXACT_MASS are retrieved from online KEGG database
  • primary affected functions: get_mz_by_KEGGcompoundIDs, get_mz_by_KEGGdrugIDs
• attributes COMPOUND, MODULE are retrieved from online KEGG database
  • primary affected function: get_mz_by_KEGGpathwayIDs
  • transitively affected functions: get_mz_by_KEGGspecies
• based on the KEGG's species code a list of pathways is retrieved from online KEGG database
  • primary affected function: get_mz_by_KEGGspecies
• legacy KEGG annotation (needs verification in case of interest)
  • all data is retrieved from various online sources: Adduct, Query.m/z, Search mass tolerance range (+/-), Metlin, Compound.Name, Chemical.Formula, Exact Mass, CASID, KEGG.Compound.ID, KEGG.Pathway.ID, KEGG.Pathway.Name, HMDB.ID, PubChem.Substance.ID, ChEBI.ID, LIPID.MAPS.ID, KEGG.Brite.Category, KEGG.Disease.ID, KEGG.Drug.ID, KEGG.Environ.ID
  • primary affected function: feat.batch.annotation.child
  • transitively affected functions: KEGG.annotationvold
• ChemSpider annotation (needs verification in case of interest)
  • all data is retrieved from various online sources: Adduct, Query.m/z, Search mass tolerance range (+/-), ChemspiderID, CommonName, Molecular.Formula, SMILES, InChI, InChIKey, AverageMass, MolecularWeight, MonoisotopicMass, NominalMass, ALogP, XLogP, Structure, KEGG.Compound.ID, HMDB, LipidMAPS, PubChem, MassBank, BioCyc, SMPDB, EPA.DSSTox, EPA.Toxcast, Pesticide.Common.Names, ChEMBL, ChEBI, NIST.Chem.WebBook, WikiPathways, DrugBank, Comparative Toxicogenomics Database, ACToR: Aggregated Computational Toxicology Resource
  • primary affected functions:chspider.batch.annotation.child
  • transitively affected functions: ChemSpider.annotation

Reference

Uppal, Karan, et al. “XMSannotator: An R Package for Network-Based Annotation of High-Resolution Metabolomics Data.” Analytical Chemistry, vol. 89, no. 2, Jan. 2017, pp. 1063–67, doi:10.1021/acs.analchem.6b01214.