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Annotate one or more observed m/z values

Source: R/MZAnnotationEngine.R
AnnotateMZ.Rd

Convenience wrapper that builds an index when one is not supplied. Reuse a pre-built index for repeated or large searches.

Usage

AnnotateMZ(
  observed_mz,
  db = NULL,
  index = NULL,
  polarity = NULL,
  adducts = NULL,
  rules = NULL,
  maldi_matrix = NULL,
  ppm = 5,
  ms1_spectrum = NULL,
  database_version = "latest",
  database_source = c("auto", "bundled", "local"),
  database_local_dir = NULL,
  infer_structure = c("auto", "never", "always"),
  structure_backend = c("auto", "native"),
  structure_workers = getOption("SpaMTP.smiles_workers", 1L),
  min_structure_score = 0.05,
  ...
)

Arguments

observed_mz

Numeric vector of observed m/z values.

db

Metabolite database used when index is NULL.

index

Optional pre-built spamtp_mz_index.

polarity

Ion mode. When NULL, infer it from index or the matrix profile, falling back to positive mode.

adducts

Optional adduct subset. When NULL, retain the complete rule space selected by the matrix profile or polarity.

rules

Optional custom rule table.

maldi_matrix

Optional MALDI matrix/reagent profile used to select rules automatically when rules is NULL.

ppm

Mass tolerance in ppm.

ms1_spectrum

Optional contextual spectrum.

database_version

Database snapshot version used when db = NULL.

database_source

Database source used when db = NULL; see LoadSpaMTPDatabase().

database_local_dir

Optional local RDS resource directory.

infer_structure, structure_backend, structure_workers, min_structure_score

Structure-aware rule-selection arguments passed to BuildMZAnnotationIndex().

...

Additional arguments passed to QueryMZAnnotationIndex().

Value

A ranked candidate data frame.

Examples

utils::str(formals(AnnotateMZ))
#> Dotted pair list of 17
#>  $ observed_mz        : symbol 
#>  $ db                 : NULL
#>  $ index              : NULL
#>  $ polarity           : NULL
#>  $ adducts            : NULL
#>  $ rules              : NULL
#>  $ maldi_matrix       : NULL
#>  $ ppm                : num 5
#>  $ ms1_spectrum       : NULL
#>  $ database_version   : chr "latest"
#>  $ database_source    : language c("auto", "bundled", "local")
#>  $ database_local_dir : NULL
#>  $ infer_structure    : language c("auto", "never", "always")
#>  $ structure_backend  : language c("auto", "native")
#>  $ structure_workers  : language getOption("SpaMTP.smiles_workers", 1L)
#>  $ min_structure_score: num 0.05
#>  $ ...                : symbol