Plot MS2 Spectra for a Single Peak in a mass_dataset Object

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.

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`.

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.

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.

Author

Xiaotao Shen xiaotao.shen@outlook.com

Examples

if (FALSE) { # \dontrun{
# Plot MS2 spectra for a peak
ms2_plots <- ms2_plot_mass_dataset(
  object = mass_object,
  variable_id = "P001",
  database = reference_database
)
} # }