Ion annotation - adelabriere/SLAW GitHub Wiki

Ion annotation in SLAW is performed using an expanded version of the cliqueMS methodology (DOI). It works by calculating the cosine similarity between EICs (Extracted ions chromatograms), building a similarity graph, and detecting complete components. To reduce computational overhead, the EICs are only extracted from a selected number of QCs files, given by ion_annotation/num_files. The components are then annotated using the InterpretMSspectrum package (DOI), which use a list of adducts also provided in the parameters.txt. The polarity of the datasets is given in the ion_annotation/polarity and the adducts are given in ion_annotation/adducts_negative, ion_annotation/main_adducts_negative and ion_annotation/adducts_positive, ion_annotation/main_adducts_positive depending of the polarity. FOr a clique to be annotated, the most intense adducts need to be one of the main_adducts adducts. The other ions will be annotated using adducts. It is possible to add more adducts by adding more rows into the adducts list. It is also used to detected the isotopes, as most ion_annotation/max_isotopes with at most a charge of ion_annotation/max_charge.

parameters :

  • polarity: (String) The polarity of the acquisition 'positive' or 'negative'
  • adducts_negative: (Strings) A list of adducts, which can be used, also including fragment. It should be 'NONE' if the data is in negative mode only. These adducts as well as all the others can be specified manually, as [M+H]+ or [M+2H]2+ for examples.
  • main_adducts_negative (Strings) A list of the main adducts, which are the authorized annotation of the most intense peaks. It should be 'NONE' if the data is in negative mode only.
  • adducts_positive: (Strings) See adducts_negative.
  • main_adducts_positive: (Strings) See main_adducts_negative.
  • dmz: (Float) Minimum mass tolerance used to annotate adducts and isotopes.
  • max_charge: (Integer) The maximum number of charges allowed, used in both raw isotopic patterns extraction data and to dereplicate features.
  • max_isotopes: (Integer) The maximum number of isotopic peaks detected, used in both raw isotopic patterns extraction data and to dereplicate features.
  • min_filter: (Integer) The minimum number of detections of features for it to be annotated. This can speed up computations if needed.
  • num_files: (Integer) The number of files used to generate EICs profile for ion annotations. This number should be at most 100 to avoid computational overhead.
  • ppm: (Float) A ppm mass tolerance is used to annotate adducts and isotopes.