annotate_single_peak_mass_dataset: Annotate a Single Peak in a mass_dataset Object

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

Annotate a Single Peak in a mass_dataset Object

Description

This function annotates a single peak in a 'mass_dataset' object using MS1 and optionally MS2 data. It allows for matching with a reference database based on m/z, retention time (RT), and MS2 fragmentation patterns.

Usage

annotate_single_peak_mass_dataset(
  object,
  variable_id,
  variable_index,
  based_on_rt = TRUE,
  based_on_ms2 = TRUE,
  add_to_annotation_table = FALSE,
  ms1.match.ppm = 25,
  ms2.match.ppm = 30,
  mz.ppm.thr = 400,
  ms2.match.tol = 0.5,
  fraction.weight = 0.3,
  dp.forward.weight = 0.6,
  dp.reverse.weight = 0.1,
  rt.match.tol = 30,
  polarity = c("positive", "negative"),
  ce = "all",
  column = c("rp", "hilic"),
  ms1.match.weight = 0.25,
  rt.match.weight = 0.25,
  ms2.match.weight = 0.5,
  total.score.tol = 0.5,
  candidate.num = 3,
  database,
  threads = 3
)

Arguments

object	A 'mass_dataset' object containing the peak data to annotate.
variable_id	The ID of the peak to annotate. Either 'variable_id' or 'variable_index' must be provided.
variable_index	The index of the peak to annotate. Either 'variable_id' or 'variable_index' must be provided.
based_on_rt	Logical, if 'TRUE' (default), retention time will be used for matching.
based_on_ms2	Logical, if 'TRUE' (default), MS2 spectra will be used for matching if available.
add_to_annotation_table	Logical, if 'TRUE', the annotation results will be added to the annotation table in the object. Defaults to 'FALSE'.
ms1.match.ppm	Numeric, mass accuracy threshold for MS1 matching in parts per million (ppm). Defaults to '25'.
ms2.match.ppm	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'.
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'.
rt.match.tol	Numeric, retention time matching tolerance in seconds. Defaults to '30'.
polarity	Character, ionization mode, either '"positive"' or '"negative"'. Defaults to '"positive"'.
ce	Character, collision energy for MS2 matching. Defaults to '"all"'.
column	Character, chromatographic column type, either '"rp"' (reverse phase) or '"hilic"'. Defaults to '"rp"'.
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'.
candidate.num	Numeric, the number of top candidates to retain for each peak. Defaults to '3'.
database	A 'databaseClass' object containing the reference spectral database for annotation.
threads	Numeric, the number of threads to use for parallel processing. Defaults to '3'.

Details

This function performs peak annotation using MS1 data and optionally MS2 data for a single peak in a 'mass_dataset' object. The matching process is based on m/z, retention time, and MS2 spectra comparison with a reference database. The results can either be returned as a data frame or added to the annotation table in the 'mass_dataset' object.

Value

Either the 'mass_dataset' object with updated annotation table or a data frame containing the annotation results for the specified peak.

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
# Annotate a single peak using MS1 and MS2 data
annotation <- annotate_single_peak_mass_dataset(
  object = mass_object,
  variable_id = "P001",
  database = reference_database,
  based_on_rt = TRUE,
  based_on_ms2 = TRUE
)

## End(Not run)

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