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

match_ms2_temp

R Documentation

Match MS2 Spectra to Library Compounds

Description

Matches an experimental MS2 spectrum against a library of reference spectra, computing similarity scores.

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`	Integer, index of the MS2 spectrum to be matched.
`ms2.info`	List, containing experimental MS2 spectra with m/z and intensity values.
`pre_match_result`	Data frame, pre-matching results containing 'Lab.ID' and 'ms2_spectrum_id'. Default is 'NULL'.
`spectra.data`	List, reference MS2 spectra library, with compound IDs as names.
`ms2.match.ppm`	Numeric, mass tolerance in parts per million (ppm) for fragment matching. Default is '30'.
`mz.ppm.thr`	Numeric, minimum m/z threshold for ppm-based error calculation. Default is '400'.
`ms2.match.tol`	Numeric, minimum score threshold for a valid MS2 match. Default is '0.5'.
`candidate.num`	Integer, number of top candidates to retain based on match scores. Default is '3'.
`fraction.weight`	Numeric, weighting factor for the fraction of matched peaks in the similarity score. Default is '0.3'.
`dp.forward.weight`	Numeric, weight for the forward dot product score in similarity calculation. Default is '0.6'.
`dp.reverse.weight`	Numeric, weight for the reverse dot product score in similarity calculation. Default is '0.1'.
`remove_fragment_intensity_cutoff`	Numeric, intensity threshold for filtering out low-intensity fragments. Default is '0'.
`masstplus_method_cutoff`	Integer, maximum number of library compounds to process using standard matching. Default is '100'.
`...`	Additional arguments (not currently used).

Details

This function performs MS2 spectrum matching by comparing a given experimental spectrum to a reference database.

- If 'pre_match_result' is provided, only the compounds in 'pre_match_result$Lab.ID' are considered. - If no pre-matched compounds are found, the function searches across all compounds in 'spectra.data'. - If the number of candidate compounds is below 'masstplus_method_cutoff', the function calculates MS2 matching scores using 'calculate_ms2_matching_score()'. - The function filters and retains the top 'candidate.num' matches with scores above 'ms2.match.tol'.

Value

A data frame containing the top candidate matches with the following columns:

`Lab.ID`	Compound ID from the reference library.
`CE`	Collision energy setting from the reference spectrum (if applicable).
`SS`	Similarity score between the experimental and library spectrum.
`ms2_spectrum_id`	ID of the experimental spectrum.