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Annotates m/z values stored in a SpaMTP Object

Source: R/MZAnnotation.R
AnnotateSM.Rd

This function assigns each valid m/z peak with one/multiple metabolite names based on the mass difference between the observed value and the theoretical value documented in the reference database. SpaMTP contains 4 cleaned reference databases to choose from these include HMDB, Lipid Maps, ChEBI and GNPS. These databases can also be combined for increased coverage.

Usage

AnnotateSM(
  data,
  db = NULL,
  assay = "Spatial",
  raw.mz.column = "raw_mz",
  ppm_error = NULL,
  adducts = NULL,
  polarity = NULL,
  tof_resolution = 30000,
  filepath = NULL,
  return.only.annotated = TRUE,
  save.intermediate = TRUE,
  min_score = 0,
  verbose = TRUE,
  maldi_matrix = NULL,
  ...
)

Arguments

data

Seurat Spatial Metabolomic Object containing m/z values for annotation.

db

Reference metabolite dataset in the form of a data.frame. When NULL, the bundled current RaMP chem_props table is used, unless a pre-built index is supplied through ....

assay

Character string defining the Seurat assay which contains the mz counts being annotated (default = "Spatial").

raw.mz.column

Character string defining the Seurat assay slot which contains the raw mz values, this is without the 'mz-' and are a vector of integers. This is setup by default when running the cardinal_to_seurat() function (default = "raw_mz").

ppm_error

Mass tolerance in ppm. If NULL, a strict 5 ppm maximum is used (or a smaller value inferred from tof_resolution). Set to zero for exact numerical matches.

adducts

Optional adduct names/notations; see AdductRules(). If NULL, use the complete rule space selected from maldi_matrix, or all validated general rules for the selected polarity when no matrix is given.

polarity

Character string defining the ion mode. When NULL, use the MALDI matrix profile default, a supplied index's mode, or positive mode when neither is available.

tof_resolution

Instrument resolving power retained for compatibility; it can only tighten, not widen, the default 5 ppm mass-accuracy threshold.

filepath

Character string of the directory to store the _annotated_mz_peaks.csv. If set to NULL no dataframe will be saved (default = NULL).

return.only.annotated

Boolean value indicating if the annotated Seurat Object should only include m/z values that were successfully annotated (default = TRUE).

save.intermediate

Boolean indicating whether to store the scored annotation result and its pipeline/RaMP provenance in @tools$mz_annotation. A compatibility copy is retained in @tools$db_3 (default = TRUE).

min_score

Minimum annotation score retained in the stored candidate table. The default 0 keeps all ppm-valid candidates so downstream pathway functions can apply a user-defined threshold without re-running annotation.

verbose

Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).

maldi_matrix

Optional MALDI matrix or derivatization reagent name. When supplied, SpaMTP selects validated matrix-specific rules automatically. adducts is optional and only restricts that automatic search space when explicitly supplied.

...

Additional indexed annotation/scoring arguments passed to annotateTable(), such as index, rules, or ms1_spectrum.

Value

A Seurat Object with m/z values annotated. These annotations are stored in the relative assay's meta.data (e.g. SeuratObj[["Spatial"]][[]])

Examples

# HMDB_db <- load("data/HMDB_1_names.rds")
# Annotated_SeuratObj <- AnnotateSM(SeuratObj, HMDB_db)