Annotates m/z values stored in a data.frame based on reference metabolite dataset

Helper function for AnnotateSM() and FishersPathwayAnalysis().

Usage

annotateTable(
  mz_df,
  db = NULL,
  ppm_error = NULL,
  adducts = NULL,
  polarity = NULL,
  tof_resolution = 30000,
  verbose = TRUE,
  index = NULL,
  rules = NULL,
  ms1_spectrum = NULL,
  use_mass_defect = TRUE,
  check_isotopes = TRUE,
  check_adduct_network = TRUE,
  min_score = 0,
  maldi_matrix = NULL
)

Arguments

mz_df

dataframe containing m/z values for annotation.

db

Reference metabolite dataset in the form of a data.frame. May be NULL when index is supplied.

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, infer it from a supplied index or MALDI matrix profile, otherwise use positive.

tof_resolution

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

verbose

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

index

Optional reusable index created by BuildMZAnnotationIndex().

rules

Optional custom adduct rule table; see AdductRules().

ms1_spectrum

Optional contextual MS1 spectrum with mz and intensity columns for isotope and adduct-family scoring.

use_mass_defect

Apply the CHO negative mass-defect penalty.

check_isotopes

Score carbon-13 and halogen isotope evidence when a contextual spectrum is supplied.

check_adduct_network

Downweight complex ions whose base monomer family is absent from the contextual spectrum.

min_score

Minimum final annotation score to retain.

maldi_matrix

Optional MALDI matrix/reagent profile used for automatic rule selection. adducts = NULL keeps the complete selected rule space.

Value

Generates an intermediate annotated m/z dataframe

Examples

### HelperFunction