plot_ms2_matching: Plot MS2 Matching Between Experimental and Library Spectra

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

Plot MS2 Matching Between Experimental and Library Spectra

Description

This function generates plots comparing MS2 spectra from experimental data with spectra from a reference database. It matches based on a set of user-specified parameters and provides visualizations with either static or interactive plots.

Usage

plot_ms2_matching(
  object,
  variable_id,
  variable_index,
  database,
  polarity,
  ms1.match.ppm = 25,
  ms2.match.ppm = 30,
  mz.ppm.thr = 400,
  remove_fragment_intensity_cutoff = 0,
  interactive_plot = FALSE
)

Arguments

object	A 'mass_dataset' object that contains MS2 data and annotations.
variable_id	Optional. A vector of variable IDs to be plotted.
variable_index	Optional. A vector of variable indices to be plotted. Either 'variable_id' or 'variable_index' must be provided.
database	A 'databaseClass' object containing reference MS2 spectra for matching.
polarity	Character. The ionization mode, either "positive" or "negative". Default is "positive".
ms1.match.ppm	Numeric. The mass-to-charge (m/z) tolerance in parts per million (ppm) for MS1 matching. Default is 25.
ms2.match.ppm	Numeric. The mass-to-charge (m/z) tolerance in parts per million (ppm) for MS2 matching. Default is 30.
mz.ppm.thr	Numeric. The m/z threshold for fragment matching. Default is 400.
remove_fragment_intensity_cutoff	Numeric. The intensity cutoff for removing low-intensity fragments. Default is 0.
interactive_plot	Logical. If TRUE, an interactive plot using plotly is returned. Default is FALSE.

Details

The function compares MS2 spectra from the experimental data (provided by the 'mass_dataset' object) to those in the reference 'database'. It generates matching plots for each of the specified variables and annotations. Users can specify either the 'variable_id' or 'variable_index' for plotting. The function supports both static and interactive visualizations.

Value

A list of plots (either static or interactive) comparing experimental and reference MS2 spectra.

Examples

## Not run: 
# Example usage:
all_plots <- plot_ms2_matching(
  object = my_mass_dataset,
  variable_id = c("pRPLC_1112", "pRPLC_1860"),
  database = my_database
)

## End(Not run)

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