Query an indexed metabolite annotation search space — QueryMZAnnotationIndex • SpaMTP

Candidates are pruned by ppm tolerance and proton/charge validity during index construction, then ranked using mass error, rule prior, mass-defect, isotope, and contextual adduct-family evidence.

Usage

QueryMZAnnotationIndex(
  observed_mz,
  index,
  ppm = 5,
  ms1_spectrum = NULL,
  use_mass_defect = TRUE,
  check_isotopes = TRUE,
  check_adduct_network = TRUE,
  min_score = 0
)

Arguments

observed_mz: Numeric vector of observed m/z values.
index: A spamtp_mz_index from BuildMZAnnotationIndex().
ppm: Mass tolerance in parts per million.
ms1_spectrum: Optional contextual spectrum with mz and intensity columns. It should represent the same retention-time window or spatial pixel/region as the queried peaks.
use_mass_defect: Apply the CHO negative mass-defect penalty.
check_isotopes: Score carbon-13 and, when relevant, chlorine/bromine M+2 patterns.
check_adduct_network: Downweight complex ions whose base monomer family is absent from ms1_spectrum.
min_score: Minimum final score to retain.

Value

A ranked candidate data frame.