match_ms2_temp: Match MS2 Spectra to Database Compounds
In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

match_ms2_temp

R Documentation

Match MS2 Spectra to Database Compounds

Description

This function matches MS2 spectra from experimental data against MS2 spectra in a database. It calculates MS2 matching scores for each compound in the database, and selects the best matches based on the provided matching parameters.

Usage

match_ms2_temp(
  idx,
  ms2.info,
  pre_match_result,
  spectra.data,
  ms2.match.ppm = 30,
  mz.ppm.thr = 400,
  ms2.match.tol = 0.5,
  candidate.num = 3,
  fraction.weight = 0.3,
  dp.forward.weight = 0.6,
  dp.reverse.weight = 0.1,
  remove_fragment_intensity_cutoff = 0,
  masstplus_method_cutoff = 100,
  ...
)

Arguments

`idx`	Numeric. The index of the current MS2 spectrum in the 'ms2.info' list.
`ms2.info`	A list of MS2 spectra, where each element is a matrix with two columns ('mz' and 'intensity').
`pre_match_result`	A data frame containing the preliminary match results from MS1 or RT matching, including compound identifiers ('Lab.ID').
`spectra.data`	A list of MS2 spectra from the database, where each element is a matrix with two columns ('mz' and 'intensity').
`ms2.match.ppm`	Numeric. Mass tolerance in parts per million (ppm) for MS2 peak matching. Default is 30.
`mz.ppm.thr`	Numeric. m/z threshold for ppm calculation. Default is 400.
`ms2.match.tol`	Numeric. Score threshold for MS2 matches. Only matches with scores above this value are retained. Default is 0.5.
`candidate.num`	Numeric. The number of top candidate annotations to retain per MS2 spectrum. Default is 3.
`fraction.weight`	Numeric. Weight for the fraction of matched fragments in the total MS2 score calculation. Default is 0.3.
`dp.forward.weight`	Numeric. Weight for the forward dot product score in the total MS2 score calculation. Default is 0.6.
`dp.reverse.weight`	Numeric. Weight for the reverse dot product score in the total MS2 score calculation. Default is 0.1.
`remove_fragment_intensity_cutoff`	Numeric. Intensity cutoff to remove low-intensity MS2 fragments from matching. Default is 0.
`...`	Additional arguments to pass to internal functions.

Details

The function takes an MS2 spectrum from the experimental data and matches it against MS2 spectra in a reference database. It computes matching scores based on the provided mass tolerance ('ms2.match.ppm'), fragment matching weight parameters ('fraction.weight', 'dp.forward.weight', 'dp.reverse.weight'), and intensity cutoff. The best-matching spectra from the database are retained and returned as candidates.

If preliminary MS1/RT matches are provided ('pre_match_result'), the function only considers those compounds for MS2 matching. Otherwise, all compounds in the database are considered.