ms2_plot_mass_dataset: Plot MS2 Spectra for a Single Peak in a mass_dataset Object

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

Plot MS2 Spectra for a Single Peak in a mass_dataset Object

Description

This function generates MS2 spectra comparison plots for a single peak in a 'mass_dataset' object by comparing experimental MS2 data with reference MS2 data from a spectral database.

Usage

ms2_plot_mass_dataset(
  object,
  variable_id,
  variable_index,
  polarity = c("positive", "negative"),
  ms1.match.ppm = 25,
  ms2.match.ppm = 30,
  mz.ppm.thr = 400,
  database,
  interactive_plot = FALSE
)

Arguments

object	A 'mass_dataset' object containing the peak data.
variable_id	The ID of the peak to plot. Either 'variable_id' or 'variable_index' must be provided.
variable_index	The index of the peak to plot. Either 'variable_id' or 'variable_index' must be provided.
polarity	Character, ionization mode, either '"positive"' or '"negative"'. Defaults to '"positive"'.
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'.
database	A 'databaseClass' object containing the reference spectral database for MS2 data.
interactive_plot	Logical, if 'TRUE', generates an interactive plot using 'plotly'. Defaults to 'FALSE'.

Details

This function retrieves the MS2 spectra for a specified peak and compares them to the reference MS2 spectra from a provided database. It generates a plot for each matched annotation, showing the experimental spectrum and the reference spectrum side by side.

Value

A list of MS2 spectra comparison plots for the specified peak, with one plot per matched annotation. If 'interactive_plot = TRUE', the plots are returned as interactive 'plotly' plots.

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
# Plot MS2 spectra for a peak
ms2_plots <- ms2_plot_mass_dataset(
  object = mass_object,
  variable_id = "P001",
  database = reference_database
)

## End(Not run)

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