identify_peak: Identify a Peak in a Mass Spectrometry Dataset

In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

Identify a Peak in a Mass Spectrometry Dataset

Description

This function identifies a potential metabolite peak in a mass spectrometry dataset by matching MS1 and MS2 data to a reference spectral database.

Usage

identify_peak(
  idx,
  ms1.info,
  ms2.info,
  spectra.info,
  spectra.data,
  ppm.ms1match = 25,
  ppm.ms2match = 30,
  mz.ppm.thr = 400,
  ms2.match.tol = 0.5,
  rt.match.tol = 30,
  ms1.match.weight = 0.25,
  rt.match.weight = 0.25,
  ms2.match.weight = 0.5,
  total.score.tol = 0.5,
  adduct.table,
  candidate.num = 3,
  fraction.weight = 0.3,
  dp.forward.weight = 0.6,
  dp.reverse.weight = 0.1,
  remove_fragment_intensity_cutoff = 0,
  ...
)

Arguments

idx	The index of the peak to identify.
ms1.info	A data frame containing MS1 information such as m/z and retention time (RT).
ms2.info	A list containing MS2 spectra data for each peak.
spectra.info	A data frame containing metadata about the reference spectra in the database.
spectra.data	A list containing the MS2 spectra data from the reference database.
ppm.ms1match	Numeric, mass accuracy threshold for MS1 matching in parts per million (ppm). Defaults to '25'.
ppm.ms2match	Numeric, mass accuracy threshold for MS2 matching in ppm. Defaults to '30'.
mz.ppm.thr	Numeric, m/z threshold in ppm for matching MS1 and MS2. Defaults to '400'.
ms2.match.tol	Numeric, tolerance for MS2 fragment ion matching. Defaults to '0.5'.
rt.match.tol	Numeric, retention time matching tolerance in seconds. Defaults to '30'.
ms1.match.weight	Numeric, weight of MS1 matching in total score calculation. Defaults to '0.25'.
rt.match.weight	Numeric, weight of RT matching in total score calculation. Defaults to '0.25'.
ms2.match.weight	Numeric, weight of MS2 matching in total score calculation. Defaults to '0.5'.
total.score.tol	Numeric, threshold for the total score. Defaults to '0.5'.
adduct.table	A data frame containing the list of adducts to be considered for matching.
candidate.num	Numeric, the number of top candidates to retain for each peak. Defaults to '3'.
fraction.weight	Numeric, weight for the MS2 fragmentation score. Defaults to '0.3'.
dp.forward.weight	Numeric, weight for the forward dot product in MS2 matching. Defaults to '0.6'.
dp.reverse.weight	Numeric, weight for the reverse dot product in MS2 matching. Defaults to '0.1'.
remove_fragment_intensity_cutoff	Numeric, intensity cutoff for removing low-intensity MS2 fragments. Defaults to '0'.
...	Additional arguments passed to other methods.

Details

This function matches experimental MS1 and MS2 data with reference spectra in a spectral database. It calculates matching scores based on m/z, RT, and MS2 fragmentation pattern similarities. The function supports matching multiple adducts and considers weights for MS1, MS2, and RT matching in the total score calculation.

Value

A data frame containing the identified peak and its matching results, including total score, m/z error, RT error, and matching scores.

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
identified_peak <- identify_peak(
  idx = 1,
  ms1.info = ms1_data,
  ms2.info = ms2_spectra,
  spectra.info = reference_spectra_info,
  spectra.data = reference_spectra_data
)

## End(Not run)

tidymass/metid documentation built on Oct. 8, 2024, 10:32 p.m.